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[hg] galaxy 2531: Renamed test files and fixed output datatype p...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d5182c4870b changeset: 2531:0d5182c4870b user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Aug 04 16:32:57 2009 -0400 description: Renamed test files and fixed output datatype problem with solid-to-fastq tool 7 file(s) affected in this change: test-data/s2fq_out1.fastqsanger test-data/s2fq_out1.tabular test-data/s2fq_out2.fastqsanger test-data/s2fq_out2.tabular test-data/s2fq_out3.fastqsanger test-data/s2fq_out3.tabular tools/next_gen_conversion/solid_to_fastq.xml diffs (1981 lines): diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out1.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out1.tabular --- a/test-data/s2fq_out1.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004/1 -AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG -+ -><C&&9952+C>5<.?<79,=42<292:<(9/-7 -@1831_573_1050/1 -TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT -+ -;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -@1831_573_1067/1 -AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG -+ -++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -@1831_573_1219/1 -CGCCCTATAATAATACAGCGCGTTAGACCGCTCA -+ -@@=4/+)5)408?'665>*/5?<61';<3,:,5- -@1831_573_1242/1 -GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC -+ ->>::>17=A5?@@=;7A=;2.60>82<8=74+;; -@1831_573_1333/1 -AGAATCGTTACCACACACTGCGTCTGGGTATCCG -+ -='@#%3=.>)/34*117,,/6-4+.9742456<) -@1831_573_1362/1 -CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC -+ -B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -@1831_573_1448/1 -TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG -+ -7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ -@1831_573_1490/1 -CTCGTCATGTTACGCAAAGGCACGTCACAGCACC -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%&#0'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-7;3#,3//#,45/#&06 -@1831_573_1853/1 -CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC -+ -4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -@1831_573_1943/1 -ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC -+ ->/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<07%1372$%<54# -@1831_574_243/1 -AGGCACCGTAACTCAGGACATTCTCGATTAGTTA -+ -@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 -@1831_574_257/1 -ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC -+ ->>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -@1831_574_293/1 -TGCTGCAAATAAACATACAGCCTTCTAATGACTA -+ -')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -@1831_574_389/1 -CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA -+ -)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -@1831_574_575/1 -TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG -+ -?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -@1831_574_592/1 -TCATTTACCACGTCAGGGTCGGAGTCATTCATTA -+ -3-5)19,,<@>4067<2.-864346;9<1/;212 -@1831_574_617/1 -AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC -+ ->@?;>?=@==@>@=5?@+@:@40@><:0)')64- -@1831_574_725/1 -GACAAGATGGCTATTATTTACAATCCGATCTGCA -+ -'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -@1831_574_734/1 -CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG -+ --&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 -@1831_574_824/1 -AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT -+ -@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -@1831_574_959/1 -CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC -+ -A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -@1831_574_1062/1 -ACCGGTAATATAAGGCAACATGATTACGGCCACG -+ -@821<//:136/8<1/5.427.;>288/0<1$)/ -@1831_574_1092/1 -GACTGGCGAAATCATCGCGGAAAAACCCCTATCA -+ -8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -@1831_574_1103/1 -ATCTCCTGATTAGACATATCTCCGTAGCTCACGC -+ -??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -@1831_574_1116/1 -CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC -+ -(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -@1831_574_1194/1 -TTATCACATTTGGGGATCGGAAGGGACTACTTCG -+ -5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -@1831_574_1204/1 -CTTACTGGTCTGCTGGACATATAGTGGCGATGAA -+ -A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* -@1831_574_1306/1 -ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA -+ -2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -@1831_574_1387/1 -GTACTTCTCAATGCTGCACTACTATGTACGCCCC -+ -?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -@1831_574_1431/1 -GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC -+ -7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -@1831_574_1560/1 -GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC -+ -))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -@1831_574_1591/1 -TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG -+ -=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -@1831_574_1624/1 -ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG -+ -<6.&(,7-+))7..'/;43.)927.(<85&13-) -@1831_574_1826/1 -TACGTCGCGACCGAGCGTTATATAGTCTGACCCC -+ -@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -@1831_574_1903/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -@1831_574_1961/1 -GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA -+ ->-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 -@1831_575_54/1 -TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA -+ -=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -@1831_575_80/1 -TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT -+ -?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -@1831_575_192/1 -AACTACGCCCCTTAATTACACAGCGCGTTAGACC -+ -:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -@1831_575_197/1 -TTCGCCTACACTTAGATACCTCTTAAACTCAATG -+ --:?463@A:88?6?437<=.2&1.;@67.4@%2, -@1831_575_223/1 -ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA -+ -?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -@1831_575_420/1 -CCCACATGGAAAACACTCACCGCCGAACAGAGCG -+ -2?.>?(-''2+..@),$%1@;')1)?+)7.').. -@1831_575_434/1 -ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC -+ -@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -@1831_575_444/1 -TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA -+ -2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -@1831_575_459/1 -CTTATCAGCACACGGTTTACCAGTCCGACTCCAA -+ -@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -@1831_575_506/1 -CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC -+ -?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -@1831_575_569/1 -AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT -+ -'9-,@29+479%&>9#&08=>7#9>,69/+'*3) -@1831_575_622/1 -CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC -+ -A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -@1831_575_644/1 -CTTGAATGGCGATCTCGTCGAGGAAATACCACTA -+ -<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -@1831_575_663/1 -GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA -+ -@@@@A</;A>@6>0792<5966:?;25+:><1,+ -@1831_575_681/1 -TCTCCTGATTAGACATATCACTGTTGAACACAGC -+ -72?.)25;96-14'*.03'#4#++$)/8+%/((& -@1831_575_711/1 -TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC -+ -%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -@1831_575_730/1 -CACACAGGAACCATAGCGTATGTTATTCACCCCC -+ -%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -@1831_575_904/1 -ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC -+ -<><.689@@7@<54:4=@>69=:+6-=42;8<:# -@1831_575_938/1 -TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA -+ -:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -@1831_575_970/1 -TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC -+ -@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -@1831_575_991/1 -TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA -+ ->>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -@1831_575_1138/1 -TTGAAAGACCTGAACGCGATTTCATGTTTACTGC -+ -=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -@1831_575_1157/1 -TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC -+ -B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 -@1831_575_1180/1 -GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA -+ -<B>5?':/78?;1;55:997@@>94=7<186->7 -@1831_575_1283/1 -GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT -+ -C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -@1831_575_1302/1 -CGACTATTCGTTTCGTCTAGAACGTGACACTAGC -+ -12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -@1831_575_1310/1 -CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT -+ -<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -@1831_575_1321/1 -CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG -+ -;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -@1831_575_1373/1 -CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA -+ -@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -@1831_575_1419/1 -TGGGGAATATAACAGCGTAGCGTTGAACACTAGA -+ -//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -@1831_575_1436/1 -TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC -+ -2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -@1831_575_1442/1 -TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG -+ ->58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -@1831_575_1454/1 -CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT -+ -4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -@1831_575_1500/1 -CACAAAAGGTCCCTACCTGTCTACCCTACATAGC -+ -?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -@1831_575_1535/1 -CTCGACGATATGACCGCCAGCCACTTAACTCCGC -+ -B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -@1831_575_1724/1 -TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA -+ -<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -@1831_575_1829/1 -CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC -+ -2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -@1831_575_1898/1 -CTTACCATATCATCTCAACCCATAACAGCACTTA -+ -B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -@1831_575_1964/1 -GACAGACCATGAGGCTGAAGACTACTAAGTGCGT -+ ->39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -@1831_576_32/1 -TACGCAACGATTTATGGCCTTATAATTGAGGCCA -+ -<>?>?=7<2)522;><<@40@>704<>5=23@+& -@1831_576_74/1 -ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA -+ -=@@?@>(??<B5?@@@9<@><+><;@';>6961? -@1831_576_86/1 -ATGAAAACGCATTAGGACAACCATAATGGCCTCA -+ -811)2:*.++5</:3+43924*))/:,6&29)2/ -@1831_576_89/1 -GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA -+ -)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -@1831_576_266/1 -ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT -+ -@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -@1831_576_327/1 -GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA -+ -@?@6@@;<@?><@>==3@:==<3@@>53<9><6= -@1831_576_331/1 -GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -+ --2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -@1831_576_387/1 -ACACGCCATGATCCGATAAGAAGGGAACGTAAGG -+ -8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -@1831_576_1019/1 -GATGCGCGCTGTCATGGCATCGAACCATCGGTCG -+ -<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -@1831_576_1068/1 -AAGAGTGACTCACTTACCGGGATGCGATGGAGCC -+ ->><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -@1831_576_1131/1 -AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA -+ -04@#@/@,4>9?2+?1571@',>=;(759;*92< -@1831_576_1168/1 -CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA -+ -@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -@1831_576_1207/1 -CAACCTGACTAAACGGGGATACGCTGGCGCTACA -+ -$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -@1831_576_1289/1 -TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT -+ -9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -@1831_576_1329/1 -CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA -+ ->&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -@1831_576_1367/1 -GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT -+ -?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -@1831_576_1416/1 -TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC -+ -';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -@1831_576_1461/1 -GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA -+ -1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -@1831_576_1605/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -@1831_576_1664/1 -CGCGCACAACTCGCCATGATACGACAAGACCCGA -+ -@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -@1831_576_1671/1 -GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT -+ -@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -@1831_576_1729/1 -CGTTTCGTCTACAACGTGACACTAGCACAGTATA -+ -?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -@1831_576_1880/1 -TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT -+ -515/792,:,7/%/05,%$):+#8%2(1754))3 -@1831_576_1982/1 -AATGTCGTCAGACGACTTTGGCGCGAAAACCATA -+ -@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -@1831_576_1987/1 -AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA -+ -##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -@1831_576_2014/1 -CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT -+ -@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -@1831_576_2028/1 -ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA -+ -<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -@1831_577_40/1 -CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT -+ -2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 -@1831_577_119/1 -TCCCACAAGCCATTGACATGCTCGCTCTAAACAG -+ ->?C11)-1/)#;#/,850*+.+$$5550+%-.40 -@1831_577_133/1 -TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG -+ -4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -@1831_577_255/1 -ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG -+ -<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -@1831_577_281/1 -TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA -+ --:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -@1831_577_288/1 -CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA -+ -;/79??&=B::298*6.7/+4&21,7,6?.7#'6 -@1831_577_322/1 -GAATGCTGGAGTACATTATGACAAACTATCGGAG -+ -=;>4506;255464-<#7+194&2<?65968)7/ -@1831_577_362/1 -CGATTAGTTACCACTCGTATTCGCACGCCCAGGA -+ -2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -@1831_577_382/1 -GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA -+ -2957/:1))=76(*24;,3+:<.&.&-=1=2/5* -@1831_577_464/1 -TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG -+ -=<7/<826)>#.'&4204+5#/041.7*91&756 -@1831_577_488/1 -TGAATAGTTATGGCCAGAATGTCTGCACCGATAC -+ -48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -@1831_577_511/1 -GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT -+ -7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -@1831_577_545/1 -ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT -+ -><<9?<>?A<481@<@8==@76/61<95.5988- -@1831_577_559/1 -GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG -+ -<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' -@1831_577_562/1 -GTTCCACTACGTTCCACGCAAAGGAATCCGAATC -+ -((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -@1831_577_637/1 -GCCTTCGCGGGAGCATATCAGTCGATACATCCCA -+ --,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -@1831_577_641/1 -TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT -+ -47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -@1831_577_692/1 -CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA -+ -B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out2.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out2.tabular --- a/test-data/s2fq_out2.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/2 -GTTCGTGGCCGGTGGGTGTTTGGG -+ -###$$#$#$&#####$'$#$###$ -@1378_17_1788/2 -TGGGTGGATGTGTTGTCGTTCATG -+ -#$#$###$#$#######$#$#### -@1378_25_2035/2 -GTGCGTCGGGGAGGGTGCTGTCGG -+ -######%#$%#$$###($###&&% -@1378_28_770/2 -GGTTGGGAGTTGGCGCGCGTGGTT -+ -###$##%%$####%#%$#%%#($$ -@1378_33_1945/2 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -.6;?;55697>8779457986264 -@1378_34_789/2 -GGGCTTGCGTTAGTGAGAGGTTGT -+ -###%$%$%%###$####$###$#& -@1378_35_263/2 -GGCGGGGGGGGGGGGGGGGGGGGG -+ -$%%&,)3/)%$-6'$&5&#$''5. -@1378_43_186/2 -GCTAGGGTTTGGGTTTGCGGTGGG -+ -$%#$########%##%#$###'#' -@1378_51_1671/2 -GGTGTTGTTCGGATGTAGCGTGGG -+ -##%$$####$########$##0## -@1378_56_324/2 -GCTGGGTGATCTAAGGAATGTAAT -+ -#$#####$$$#$$$$##%###*(# -@1378_56_773/2 -TCTGGTCGGTTTCGGGGAGTGGAA -+ -##%%#&$###$#$##%$####%%$ -@1378_62_2027/2 -GTTGGCCTGGCCTGCCGTGCTGCG -+ -*##),/%##$)#%##1$#'%.#&# -@1378_62_2029/2 -GGCGGTGTGTGGTGCGGCTGTGCG -+ -/$$$=(####%####)$$%$-&%# -@1378_67_1795/2 -CGTGCCAACGACCGTCCTACGGAG -+ -@@.?7@@@.@:@A<<>>=>70<@7 -@1378_68_466/2 -GTGTCATCTGAGGTAAAGCATTGT -+ -/##$09#$#.=$#$76+$%1'### -@1378_68_1692/2 -TGTTCGATTTAGGTCTTGCCTCGC -+ -###%%$%%##%$#$##$###$$#$ -@1378_80_664/2 -TGTCTGCGTTGTATCTCTGGTGTA -+ -%##%,%$$#&$$###$#$%##'%# -@1378_85_1786/2 -CCCTAGGAGCGTATACCGGACGAG -+ -,'&/%/@,&1,&'/)&,6&&1)(( -@1378_86_1011/2 -AGGCGATGGGATATTATTTTACTT -+ -:$###)%##$9$###1$$#$2### -@1378_86_1789/2 -GGCCAGGTACTAATAAATTCAACA -+ -1.51/&%#'$,*?%#6&0$$5,20 -@1378_91_1596/2 -GCTTTTTCATTCGGTGCCTTTGGA -+ -'>%/3%=()8'#.%?50$&5>%)% -@1378_94_1595/2 -GCGGGTTAACCCAGTACCTCTGGC -+ -,8@6'>8<76>@@(->9)7'*941 -@1378_95_1039/2 -GTTCTGTGCCAGGTGAGGTACGGA -+ -&##,./#$&)6##+,'#$$0(##$ -@1378_95_1767/2 -CTAATTGACCGGGCAAGCTATTAA -+ -',,2'(10/>:=/7).3&%6&)&6 -@1378_96_1037/2 -CTGCTGGGCCATTTGACTTACTCA -+ -'$#+#(##-%5##+*&###-.$$$ -@1378_96_1764/2 -TCTTTGTAACCCACTTAGTATTTC -+ -4='28>.@4881B807:822>%)1 -@1378_98_1574/2 -AGGCGAGTGTGGGGGTTGTTTGAG -+ -+%%$#)##%##$####%###$%$# -@1378_107_1647/2 -GGTCTGGTTCTATGTTGGTCGACT -+ -###'$$#$$$(#%###(#$##$%# -@1378_111_829/2 -GGTCTTCTATGGTGCTAAATTAGT -+ -$##'&###$##)#%($#$%#$'%# -@1378_111_1900/2 -GCACGCCTTTGGGCTAAGCCGTAA -+ -)$)'#%$########$'#&%$#(# -@1378_112_1483/2 -TGGAGTGGTGTGTTTGCTGAGCCA -+ -#$#)#############$#%#%'% -@1378_125_1287/2 -TGACGTGGGTTGTCCCGTGAGATT -+ -##$%%#$###$##$$#&%##$(%% -@1378_126_468/2 -AAAAAACGGGCCGGGCGGACTAGG -+ -@@B@@@>@2>1+?:92)>@8&&<+ -@1378_127_664/2 -TCGCTTTGCCTATGTTTGTTCGGA -+ -#%$%#&##$%#%%###$$###)-' -@1378_129_463/2 -AAAAAAAAAAAAAAAAAAAAAAAA -+ -,)&20%8'(&35-***1-2&+510 -@1378_129_875/2 -GACCTTTACGTATTGGGGGTTGGC -+ -###)###+###$##$#&%##$,#$ -@1378_140_1251/2 -TTTCCTTCGTGTGCGTGCGGAGTG -+ -#%#%$##$$$######.$$$%#%( -@1378_141_809/2 -TCTCGTGGTTTCTTTTTTATGTGT -+ -##%)##$$#####%$#$#%%#'## -@1378_144_983/2 -GTTCGTTCGTGGTGTACGAGGGTG -+ -#(#%#####($#%##$$#%##%#) -@1378_153_270/2 -GGCCGTGTGCGGGTGTAGATTGGA -+ -%$##($######&##$&$$$$%## -@1378_155_1689/2 -CGCGTTCGGACAAAGCTAGCACCT -+ -@4@@=6=@@<4:@@681@@@.24. -@1378_157_1580/2 -GGGATTGAAGGGATGTATGCTAGG -+ -#%$&%#$$'%$%#$##*#%$$$$# -@1378_161_317/2 -AATCCATACCCACAAAAGCAGGCC -+ -.&%','(@''?7//+&)+2.+)0) -@1378_177_735/2 -CGAGCCCTAAACCATGAGATCGGA -+ -@@B>@AC9@A<B8@=9>7@5)>,0 -@1378_181_1684/2 -TTTCTGTTGTGGTTTTGTTGGGGT -+ -$##'$%'##%##$%$#$$####$* -@1378_187_1407/2 -TTGGGTGAAATCTTGTCGAGTGGA -+ -####&##$$###$#####%##%%) -@1378_203_721/2 -CCTTTACGATCATAAACCATGACC -+ -9<&./1&@;12')?<1',?/)&/. -@1378_206_2039/2 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -?=>>?=:;<>>4::<=56199(05 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out3.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out3.tabular --- a/test-data/s2fq_out3.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/1 -AGACCGGGCGGGGTGGCGTTCGGT -+ -%##+'#######%###$#$##$(# -@1378_17_1788/1 -TGCCGTGTCTTGCTAACGCCGATT -+ -#'#$$#$###%%##$$$$###### -@1378_25_2035/1 -CTGCGTGTTGGTGTCTACTGGGGT -+ -#%#'##$#$##&%#%$$$%#%#'# -@1378_28_770/1 -CTGCTATGCCGGCCGCCTGCCCCT -+ -%##(#$$#%$#$%###$%%$##$# -@1378_33_1945/1 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -+9;64287788752796/576352 -@1378_34_789/1 -ATGGTGGCTGACGCGTTTGACTGT -+ -#$##%#$##$&$#%##$##$###$ -@1378_35_263/1 -GGGCGGGGGGCGGCGGGGGGGGGG -+ -),,#%'$)'-(%&%'%',%%&&(& -@1378_43_186/1 -ATACTAGTTGGGACGCGTTGTGCT -+ -#$(4%$########$#$###$$$# -@1378_51_1671/1 -TGGGTAGGTGCGGCTCTTGCGGTC -+ -##$#$%###%%#%#$##$$##### -@1378_56_324/1 -AGGCTTGGATTGTTGCGCTGACCT -+ -/+#**###%%##%#####$$$#$# -@1378_56_773/1 -TGTCGTGAGGTCACTTATCCCCAT -+ -&%#%##%%#####&#$%##$%##$ -@1378_62_2027/1 -CTTCCACGATCTGCTCGCTGTGGT -+ -(#&&$##$$#$%#%$$$#$###'# -@1378_62_2029/1 -TCTGGGCTGTCTTCGGGTCGGTGT -+ -$%$$####$##$$#)##%%#$### -@1378_67_1795/1 -TAGTGGGCTAGTCCGGGATCTACC -+ -B@C2@@?;-@@1>'A@@91@.@1' -@1378_68_466/1 -GTGATCGTCGGTGCCAGTCCCTGT -+ -#(%)+##$#$#%#+$%##$##### -@1378_68_1692/1 -GGTCTTCTGGGCACGGGCCAAGTT -+ -###)%'&%##$###%#######$# -@1378_80_664/1 -CTGCTTTGATCCCCGGTGGAGCAC -+ -7#%###$$6#######$##$$$## -@1378_85_1786/1 -ATACTATGTCGATCTGTAAAAAAA -+ -)&.)#3%(a)$&%-,2#&+.-%0&./ -@1378_86_1011/1 -CTACGTTATTGCTCTGTTTGTCCT -+ -######$%##$$$%###%#$#### -@1378_86_1789/1 -CGAATATCCCCTGGTTTAGAAGTA -+ -61?1;@/>@<=/(.7'(<5@=%$= -@1378_91_1596/1 -TTAGCGGTTGACTATCTGCTGACA -+ -*&+'#9'(%*'#//,&<),/)'*# -@1378_94_1595/1 -CGTGCGACAGCCCATGTTTTCAGA -+ --=..5,3826&*+.+#+#%%6;%# -@1378_95_1039/1 -CGGCGTCCATCTTCGCCTTGAGAT -+ -$##.#$##$$#%$#$%%$###$)$ -@1378_95_1767/1 -ACACGCACCATCTGGCGGCTAACC -+ -86<65<4<C27/$5+#;-$+#2%$ -@1378_96_1037/1 -ATCCCCCAAGATGCCTGTTGATTG -+ -$#$'##$$$#%$$#%###+##$#$ -@1378_96_1764/1 -TACACCGGAACCTTGCACTAAAGC -+ -6-9'<#+81?+*<8-=69&6;*3) -@1378_98_1574/1 -GTTCTGCCGGTGTCTGTGGCGGGC -+ -$$#+&$$####%$$$###$%#%%# -@1378_107_1647/1 -AGGCCTACTACGCGTCATTGATAG -+ -&#$$#$(.#%#$$####&$%##($ -@1378_111_829/1 -TGCGGCACTTGCTTCTTCGTATTT -+ -%#%##%#$%#$#%###$$##&#$$ -@1378_111_1900/1 -TCCCCTCGCTCGGCTCTGTGCTGT -+ -$&%*$#(#)##$#'##%(##$#$% -@1378_112_1483/1 -TGTCCAGCTATGCGGCTTCCTCCT -+ -%#$+#%#&#$#####%####%$## -@1378_125_1287/1 -TGTCTCTGGGGGGCCTGGTTAGGT -+ -$##13$'%#$###$$###$$$#&# -@1378_126_468/1 -TCTCCTGATTAGACATATCTCCGT -+ -7>@318?=,=8@49579?..7,7) -@1378_127_664/1 -AGAGGTTGGTGTCTTGTCGCAGCT -+ -##'#$######$$%######$$$# -@1378_129_463/1 -CCTGTGGGCCAAGCCCAATGAAAG -+ -8),,<6(--)<()5&.&/8+;.2+ -@1378_129_875/1 -TTTCTATGGCTTACGCTGTCTGCC -+ -#$($##%####%$#$#####$### -@1378_140_1251/1 -ATCCTAGCGCGGTGTCTTGGGGAC -+ -#$%1#$$$##$##$#$#$##$%$$ -@1378_141_809/1 -TGTCCTCCAGTGTCTGTTGGGTGT -+ -%&,-##$$#(%###$#$$'###'# -@1378_144_983/1 -AGCGCCCGGTTGGTGCGGCTCGTC -+ --$(&%*$#*#))#$$$#%%$#$## -@1378_153_270/1 -AGTCCTTGTCCCCTGGGTTTTCCC -+ -+''$#&%$%#$##&$$($#&#$$# -@1378_155_1689/1 -TTGGGAGGGAGAGAGACTAGACCG -+ -?4@@4<<??<?-@4@=4<5<?:/> -@1378_157_1580/1 -TGGGCCTCGGTGCCCTTGGTCTGT -+ -#%)$##'#$$$&#####%#$#$## -@1378_161_317/1 -TTGGCCGGCAACCCCGGTACCTAA -+ -7<,<'@)@>.)2@/')'&(?/-<( -@1378_177_735/1 -AGTACGCCATGTATTTGCGACCAG -+ -=?@?C<88@=>:7>@55/.,416, -@1378_181_1684/1 -CGACTCCCGCATTCACGGTCAAGT -+ -&*#,##$#&$*$$#$#$$$#%$## -@1378_187_1407/1 -TGGCGTCCACTCGTGGGTCTATCG -+ -$#$'%#$%$%&$%#####$#$#%# -@1378_203_721/1 -CCTAAATAACCCAGGGTAAAAGAT -+ -9<1+2+1@=259@+;2.71&@+2& -@1378_206_2039/1 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -9@?8>;>>><<994;=895895-8 diff -r dd1b55dd3c22 -r 0d5182c4870b tools/next_gen_conversion/solid_to_fastq.xml --- a/tools/next_gen_conversion/solid_to_fastq.xml Tue Aug 04 12:05:12 2009 -0400 +++ b/tools/next_gen_conversion/solid_to_fastq.xml Tue Aug 04 16:32:57 2009 -0400 @@ -38,17 +38,18 @@ </inputs> <outputs>  - <data name="output1" format="tabular"/> - <data name="output2" format="tabular"> + <data name="output1" format="fastqsanger"/> + <data name="output2" format="fastqsanger"> <filter>paired['pairedSingle'] == 'paired'</filter> </data> </outputs> <tests> -  </tests>

1 0

[hg] galaxy 2532: Allow nested groupings in testing framework.
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f0978599ba8d changeset: 2532:f0978599ba8d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 05 08:58:23 2009 -0400 description: Allow nested groupings in testing framework. 3 file(s) affected in this change: test-data/joiner_out3.bed test/functional/test_toolbox.py tools/filters/joiner.xml diffs (171 lines): diff -r 0d5182c4870b -r f0978599ba8d test-data/joiner_out3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joiner_out3.bed Wed Aug 05 08:58:23 2009 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + X X X X X X +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + X X X X X X +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - X X X X X X +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + X X X X X X +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - X X X X X X +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - X X X X X X +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + X X X X X X +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - X X X X X X +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + X X X X X X +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + X X X X X X +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - X X X X X X +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + X X X X X X +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - X X X X X X +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - X X X X X X +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + X X X X X X +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - X X X X X X +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - diff -r 0d5182c4870b -r f0978599ba8d test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Aug 04 16:32:57 2009 -0400 +++ b/test/functional/test_toolbox.py Wed Aug 05 08:58:23 2009 -0400 @@ -65,52 +65,39 @@ def shortDescription( self ): return self.name - def __expand_grouping( self, tool_inputs, declared_inputs, repeat_index=0, repeat_sep='' ): + def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ): expanded_inputs = {} for key, value in tool_inputs.items(): - if isinstance(value, grouping.Conditional): - for i, case in enumerate(value.cases): - if declared_inputs[value.test_param.name] == case.value: + if isinstance( value, grouping.Conditional ): + if prefix: + new_prefix = "%s|%s" % ( prefix, value.name ) + else: + new_prefix = value.name + for i, case in enumerate( value.cases ): + if declared_inputs[ value.test_param.name ] == case.value: if isinstance(case.value, str): - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, value.test_param.name ) - else: - cond_sep = "%s|%s" % ( value.name, value.test_param.name ) - expanded_inputs[ cond_sep ] = case.value.split( "," ) + expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value.split( "," ) else: - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, value.test_param.name ) - else: - cond_sep = "%s|%s" % ( value.name, value.test_param.name ) - expanded_inputs[ cond_sep ] = case.value + expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value for input_name, input_value in case.inputs.items(): - if isinstance(input_value, grouping.Conditional): - expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=repeat_sep ) ) - elif isinstance(declared_inputs[input_name], str): - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, input_name ) - else: - cond_sep = "%s|%s" % ( value.name, input_name ) - expanded_inputs.update( { cond_sep : declared_inputs[ input_name ].split( "," ) } ) - else: - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, input_name ) - else: - cond_sep = "%s|%s" % ( value.name, input_name ) - expanded_inputs.update( { cond_sep : declared_inputs[ input_name ] } ) + expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, prefix = new_prefix ) ) elif isinstance( value, grouping.Repeat ): - for r_name, r_value in value.inputs.items(): - repeat_sep = "%s_%d|%s" % ( value.name, repeat_index, r_name ) - if isinstance( r_value, grouping.Conditional ): - cond_sep = repeat_sep + "|" - expanded_inputs.update( self.__expand_grouping( { r_name:r_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=cond_sep ) ) - else: - expanded_inputs.update( { repeat_sep : [ declared_inputs[ r_name ] ] } ) - repeat_index += 1 + for repeat_index in xrange( 0, 1 ): #need to allow for and figure out how many repeats we have + for r_name, r_value in value.inputs.iteritems(): + new_prefix = "%s_%d" % ( value.name, repeat_index ) + if prefix: + new_prefix = "%s|%s" % ( prefix, new_prefix ) + expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value }, declared_inputs, prefix = new_prefix ) ) elif isinstance(declared_inputs[value.name], str): - expanded_inputs[value.name] = declared_inputs[value.name].split(",") + if prefix: + expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name].split(",") + else: + expanded_inputs[value.name] = declared_inputs[value.name].split(",") else: - expanded_inputs[value.name] = declared_inputs[value.name] + if prefix: + expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name] + else: + expanded_inputs[value.name] = declared_inputs[value.name] return expanded_inputs def get_testcase( testdef, name ): diff -r 0d5182c4870b -r f0978599ba8d tools/filters/joiner.xml --- a/tools/filters/joiner.xml Tue Aug 04 16:32:57 2009 -0400 +++ b/tools/filters/joiner.xml Wed Aug 05 08:58:23 2009 -0400 @@ -98,7 +98,7 @@ <param name="fill_empty_columns_switch" value="no_fill"/> <output name="out_file1" file="joiner_out2.bed"/> </test> - + </test> </tests> <help>

1 0

[hg] galaxy 2530: Changes to browse_library UI, removed nested t...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dd1b55dd3c22 changeset: 2530:dd1b55dd3c22 user: James Taylor <james(a)jamestaylor.org> date: Tue Aug 04 12:05:12 2009 -0400 description: Changes to browse_library UI, removed nested tables so widths can be variable. Cleaned up some styles (more grid-like) 3 file(s) affected in this change: static/june_2007_style/blue/library.css static/june_2007_style/library.css.tmpl templates/library/browse_library.mako diffs (568 lines): diff -r 5003b7d10ff5 -r dd1b55dd3c22 static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css Mon Aug 03 17:35:44 2009 -0400 +++ b/static/june_2007_style/blue/library.css Tue Aug 04 12:05:12 2009 -0400 @@ -12,4 +12,6 @@ pre.peek{background:white;color:black;width:100%;overflow:auto;} pre.peek th{color:white;background:#023858;} a.expandLink{text-decoration:none;} -span.expandLink{width:100%;height:100%;display:block;} +span.expandLink{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png);} +.folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png);} +.folderRow span.rowIcon{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} diff -r 5003b7d10ff5 -r dd1b55dd3c22 static/june_2007_style/library.css.tmpl --- a/static/june_2007_style/library.css.tmpl Mon Aug 03 17:35:44 2009 -0400 +++ b/static/june_2007_style/library.css.tmpl Tue Aug 04 12:05:12 2009 -0400 @@ -69,7 +69,22 @@ } span.expandLink { - width: 100%; - height: 100%; - display: block; + width: 16px; + height: 16px; + display: inline-block; + vertical-align: middle; + background: url(../images/silk/resultset_next.png); } + +.folderRow.expanded span.expandLink { + background: url(../images/silk/resultset_bottom.png); +} + +.folderRow span.rowIcon { + width: 16px; + height: 16px; + display: inline-block; + vertical-align: middle; + background: url(../images/silk/folder.png); +} + diff -r 5003b7d10ff5 -r dd1b55dd3c22 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Mon Aug 03 17:35:44 2009 -0400 +++ b/templates/library/browse_library.mako Tue Aug 04 12:05:12 2009 -0400 @@ -1,5 +1,5 @@ <%inherit file="/base.mako"/> -<%namespace file="common.mako" import="render_dataset" /> +## <%namespace file="common.mako" import="render_dataset" /> <%namespace file="/message.mako" import="render_msg" /> <% from galaxy import util %> @@ -10,102 +10,144 @@ </%def> <% + def name_sorted( l ): return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) ) + +class RowCounter( object ): + def __init__( self ): + self.count = 0 + def increment( self ): + self.count += 1 + def __str__( self ): + return str( self.count ) + %> <script type="text/javascript"> $( document ).ready( function () { - // Check/uncheck boxes in subfolders. - $("input.folderCheckbox").click( function() { - if ( $(this).is(":checked") ) { - //$(this).parent().children().find("input[type=checkbox]").each( function() { this.checked = true; }); - $(this).parent().next("ul").find("input[type=checkbox]").each( function() { this.checked = true; }); - } else { - //$(this).parent().children().find("input[type=checkbox]").each( function() { this.checked = false; }); - $(this).parent().next("ul").find("input[type=checkbox]").each( function() { this.checked = false; }); - } - }); - // If you uncheck a lower level checkbox, uncheck the boxes above it - // (since deselecting a child means the parent is not fully selected any - // more). - $("input[type=checkbox]").click( function() { - if ( ! $(this).is(":checked") ) { - //var folder_rows = $(this).parents("ul").next("li.folderRow"); - //var folder_rows = $(this).parents("ul").children("li.folderRow"); - var folder_rows = $(this).parents("ul").prev("li.folderRow"); - //$(folder_rows).children("input[type=checkbox]").not(this).each( function() { - $(folder_rows).find("input[type=checkbox]").each( function() { - this.checked = false; + $("#library-grid").each( function() { + // Recursively fill in children and descendents of each row + var process_row = function( q, parents ) { + // Find my index + var index = $(q).parent().children().index( $(q) ); + // Find my immediate children + var children = $(q).siblings().filter( "[parent='" + index + "']" ); + // Recursively handle them + var descendents = children; + children.each( function() { + child_descendents = process_row( $(this), parents.add( q ) ); + descendents = descendents.add( child_descendents ); }); - } - }); - // Handle the hide/show triangles - $("span.expandLink").wrap( "<a href='#' class='expandLink'></a>" ).click( function() { - var contents = $(this).parents("li:first").next("ul"); - if ( this.id == "libraryRow" ) { - var icon_open = "${h.url_for( '/static/images/silk/book_open.png' )}"; - var icon_closed = "${h.url_for( '/static/images/silk/book.png' )}"; - } else { - var icon_open = "${h.url_for( '/static/images/silk/folder_page.png' )}"; - var icon_closed = "${h.url_for( '/static/images/silk/folder.png' )}"; - } - if ( contents.is(":visible") ) { - contents.slideUp("fast"); - $(this).find("img.expanderIcon").each( function() { this.src = "${h.url_for( '/static/images/silk/resultset_next.png' )}"; }); - $(this).find("img.rowIcon").each( function() { this.src = icon_closed; }); - } else { - contents.slideDown("fast"); - $(this).find("img.expanderIcon").each( function() { this.src = "${h.url_for( '/static/images/silk/resultset_bottom.png' )}"; }); - $(this).find("img.rowIcon").each( function() { this.src = icon_open; }); - } - }); - // Hide all dataset bodies - $("div.historyItemBody").hide(); - // Handle the dataset body hide/show link. - $("div.historyItemWrapper").each( function() { - var id = this.id; - var li = $(this).parent(); - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - li.removeClass( "datasetHighlighted" ); - } - else { - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - li.addClass( "datasetHighlighted" ); - } - return false; - }); + // Set up expand / hide link + $(q).find( "span.expandLink").wrap( "<a href='#' class='expandLink'></a>" ).click( function() { + if ( children.is( ":visible" ) ) { + descendents.hide(); + descendents.removeClass( "expanded" ); + q.removeClass( "expanded" ); + // expanded = false; + } else { + children.show(); + q.addClass( "expanded" ); + // expanded = true; + } + }); + // Check/uncheck boxes in subfolders. + q.children( "td" ).children( "input[type=checkbox]" ).click( function() { + if ( $(this).is(":checked") ) { + descendents.find( "input[type=checkbox]").attr( 'checked', true ); + } else { + descendents.find( "input[type=checkbox]").attr( 'checked', false ); + // If you uncheck a lower level checkbox, uncheck the boxes above it + // (since deselecting a child means the parent is not fully selected any + // more). + parents.children( "td" ).children( "input[type=checkbox]" ).attr( "checked", false ); + } + }); + // return descendents for use by parent + return descendents; + } + $(this).find( "tbody tr" ).not( "[parent]").each( function() { + descendents = process_row( $(this), $([]) ); + descendents.hide(); + }); }); }); </script> -<![if gte IE 7]> -<script type="text/javascript"> - $( document ).ready( function() { - // Add rollover effect to any image with a 'rollover' attribute - preload_images = {} - $( "img[rollover]" ).each( function() { - var r = $(this).attr('rollover'); - var s = $(this).attr('src'); - preload_images[r] = true; - $(this).hover( - function() { $(this).attr( 'src', r ) }, - function() { $(this).attr( 'src', s ) } - ) - }) - for ( r in preload_images ) { $( "<img>" ).attr( "src", r ) } - }) -</script> -<![endif]> +<%def name="render_dataset( library_dataset, selected, library, pad, parent, row_conter )"> + <% + ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu + ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always + ## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes + ## from the ldda. + ldda = library_dataset.library_dataset_dataset_association + if ldda.user: + uploaded_by = ldda.user.email + else: + uploaded_by = 'anonymous' + if ldda == ldda.library_dataset.library_dataset_dataset_association: + current_version = True + else: + current_version = False + %> -<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id )"> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${pad+20}px;"> + + + %if selected: + <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> + %else: + <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> + %endif + + <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + + <div popupmenu="dataset-${ldda.id}-popup"> + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + %else: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a> + %endif + ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use + ##%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=ldda.library_dataset ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + ##%endif + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + %if current_version and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + %endif + %endif + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + %endif + </div> + + </td> + <td>${ldda.message}</td> + <td>${uploaded_by}</td> + <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + </tr> + + <% + my_row = row_counter.count + row_counter.increment() + %> + + +</%def> + + +<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, parent=None, row_counter=None )"> <% def show_folder(): if trans.app.security_agent.check_folder_contents( trans.user, folder ) or trans.app.security_agent.show_library_item( trans.user, folder ): @@ -119,27 +161,36 @@ else: pad = folder_pad + 20 if folder_pad == 0: - expander = "/static/images/silk/resultset_bottom.png" - folder_img = "/static/images/silk/folder_page.png" subfolder = False else: - expander = "/static/images/silk/resultset_next.png" - folder_img = "/static/images/silk/folder.png" subfolder = True created_ldda_id_list = util.listify( created_ldda_ids ) if created_ldda_id_list: created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ] + my_row = None %> %if not root_folder: - <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"> - <input type="checkbox" class="folderCheckbox" style="float: left;"/> - <div class="rowTitle"> - <span class="expandLink"><img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder_img )}" class="rowIcon"/> + <tr class="folderRow libraryOrFolderRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${folder_pad}px;"> + + <span class="expandLink"></span> + + <input type="checkbox" class="folderCheckbox"/> + + <span class="rowIcon"></span> + ${folder.name} %if folder.description: <i>- ${folder.description}</i> %endif + <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="folder_img-${folder.id}-popup"> %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> @@ -167,125 +218,135 @@ %endif </div> </div> - </li> + <td colspan="3"></td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> %endif - %if subfolder: - <ul id="subFolder" style="display: none;"> - %else: - <ul> - %endif - %for child_folder in name_sorted( folder.active_folders ): - ${render_folder( child_folder, pad, created_ldda_ids, library_id )} - %endfor - %for library_dataset in name_sorted( folder.active_datasets ): - <% - selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids - %> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ): - <li class="datasetRow" style="padding-left: ${pad + 20}px;">${render_dataset( library_dataset, selected, library )}</li> - %endif - %endfor - </ul> + + %for child_folder in name_sorted( folder.active_folders ): + ${render_folder( child_folder, pad, created_ldda_ids, library_id, my_row, row_counter )} + %endfor + %for library_dataset in name_sorted( folder.active_datasets ): + <% + selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids + %> + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ): + ${render_dataset( library_dataset, selected, library, pad, my_row, row_counter )} + %endif + %endfor </%def> -<h2>Library '${library.name}'</h2> +<h2>Library “${library.name}”</h2> -%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <ul class="manage-table-actions"> - %if not deleted: - <li> - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> - </li> - %endif - </ul> -%endif +<ul class="manage-table-actions"> + + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + %if not deleted: + <li> + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> + </li> + %endif + %endif + + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a></li> + %else: + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li> + %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ## %endif + ##%else: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ## %endif + ##%endif + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): + <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li> + %endif + +</ul> %if msg: ${render_msg( msg, messagetype )} %endif <form name="import_from_library" action="${h.url_for( controller='library', action='datasets', library_id=library.id )}" method="post"> - <ul> - <li class="libraryRow libraryOrFolderRow"> - <div class="rowTitle"> - <% - library_item_ids = {} - library_item_ids[ 'library' ] = library.id - %> - <table cellspacing="0" cellpadding="0" border="0" width="100%" class="libraryTitle"> - <tr> - <th width="*"> - <span class="expandLink" id="libraryRow"><img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - ${library.name} - %if library.description: - <i>- ${library.description}</i> - %endif - <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="library-${library.id}-popup"> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a> - %endif - ## TODO: temporarily eliminating templates until we have the new forms features done - ##%if library.library_info_template_associations: - ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): - ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - ## %endif - ##%else: - ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - ## %endif - ##%endif - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a> - %endif - </div> - </span> - </th> - <th width="500">Information</th> - <th width="150">Uploaded By</th> - <th width="60">Date</th> - </tr> - </table> - </div> - </li> - <ul> - ${render_folder( library.root_folder, 0, created_ldda_ids, library.id )} - </ul> - <br/> - </ul> - <select name="do_action" id="action_on_datasets_select"> - %if default_action == 'add': - <option value="add" selected>Import selected datasets into your current history</option> - %else: - <option value="add">Import selected datasets into your current history</option> - %endif - %if default_action == 'manage_permissions': - <option value="manage_permissions" selected>Edit selected datasets' permissions</option> - # This condition should not contain an else clause because the user is not authorized - # to manage dataset permissions unless the default action is 'manage_permissions' - %endif - %if 'bz2' in comptypes: - <option value="tbz" - %if default_action == 'download': - selected - %endif> - >Download selected datasets as a .tar.bz2 file</option> - %endif - %if 'gz' in comptypes: - <option value="tgz">Download selected datasets as a .tar.gz file</option> - %endif - %if 'zip' in comptypes: - <option value="zip">Download selected datasets as a .zip file</option> - %endif - </select> - <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> + + <% + library_item_ids = {} + library_item_ids[ 'library' ] = library.id + %> + + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <thead> + + <tr class="libraryTitle"> + <th style="padding-left: 42px;">Name</th> + <th>Information</th> + <th>Uploaded By</th> + <th>Date</th> + </thead> + </tr> + + <% row_counter = RowCounter() %> + + ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, Nonw, row_counter )} + + <tfoot> + + <tr> + <td colspan="4" style="padding-left: 42px;"> + + For selected items: + + <select name="do_action" id="action_on_datasets_select"> + %if default_action == 'add': + <option value="add" selected>Import into your current history</option> + %else: + <option value="add">Import into your current history</option> + %endif + %if default_action == 'manage_permissions': + <option value="manage_permissions" selected>Edit permissions</option> + # This condition should not contain an else clause because the user is not authorized + # to manage dataset permissions unless the default action is 'manage_permissions' + %endif + %if 'bz2' in comptypes: + <option value="tbz" + %if default_action == 'download': + selected + %endif> + >Download as a .tar.bz2 file</option> + %endif + %if 'gz' in comptypes: + <option value="tgz">Download as a .tar.gz file</option> + %endif + %if 'zip' in comptypes: + <option value="zip">Download as a .zip file</option> + %endif + </select> + <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> + + </td> + + </tr> + + </tfoot> + + </table> + </form> + +## Help about compression types %if len( comptypes ) > 1: <div>

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Re: [galaxy-dev] manage_db: MySQL error 1059
by Nate Coraor 05 Aug '09

05 Aug '09

Hi Pieter, I moved this over to the galaxy-dev list since it's related to a local installation. Pieter Neerincx wrote: > Hi, > > I upgraded today from a Galaxy release from about a month ago and got > this error when I ran the manage_db script: > > 7 -> 8... done > 8 -> 9... done > 9 -> 10... > done > 10 -> 11... done > > This is with MySQL 5.0.45-7.el5 (on CentOS 5.3). Manual inspection > shows that despite the error the table was created: > and I have the following indices on this table: > I guess that the ix_hdadaa_history_dataset_association_id is the > abbreviated name for > ix_history_dataset_association_display_at_authorization_update_time... > or not? The question is can I safely ignore the update error or do I > have a problem? Database version 11 was created to fix the problem in 10. MySQL has a name length limit and thus the index has to be manually created. You can safely ignore these errors. --nate

1 0

Bar charts
by Pieter Neerincx 05 Aug '09

05 Aug '09

Hi, The bar chart generator does not work for me. It looks like gnuplot is complaining (see below or attached screenshot), but I'm not sure if this is the problem. I'm on CentOS 5.3 and have gnuplot version 4.0.0-14.el5. In addition I installed gnuplot-py 1.8. How do I fix this? Cheers, Pi gnuplot> set style histogram clustered gap 5 title offset character 0, 0, 0 ^ line 0: expecting 'data', 'function', 'line', 'fill' or 'arrow' line 0: undefined variable: in line 0: undefined variable: invert gnuplot> set style data histograms ^ line 0: expecting 'lines', 'points', 'linespoints', 'dots', 'impulses', 'yerrorbars', 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps', 'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars', 'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines', 'yerrorlines', 'xyerrorlines', 'pm3d' gnuplot: unable to open display 'localhost:13.0' gnuplot: X11 aborted. ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

3 3

Re: [galaxy-dev] [galaxy-user] custom tool output path
by James Taylor 04 Aug '09

04 Aug '09

Paul, This would break a lot of things in Galaxy. Everything expects that a tool output is a "Dataset", and that it has a corresponding file with its contents under "file_path". Changing this would be complex and have far reaching consequences, though not impossible (on a per tool basis, the directory where the output is deposited would be changes, and the dataset would be setup pointing to the right place, however this affects how datasets get shared to the cluster among other things). Maybe it would help to better understand what you want to accomplish by doing this. (Moved to galaxy-dev since this is about framework internals not using the galaxy interface). -- jt On Aug 4, 2009, at 11:35 AM, Paul Rigor (prigor@uci) wrote: > But in defining a tool, can the default path be overridden by > assigning a different path to a variable, eg, $outputpath? > > Thanks, > paul > > On Tue, Aug 4, 2009 at 5:07 AM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Paul Rigor (prigor@uci) wrote: > > For custom tools, I was wondering how the output path can be set in > the xml file describing the tool? Are there 'default' variables I > should be aware of in order to use as the output path the > "user_library_import_dir = database/users" in my universe_wsgi.ini? > > Hi Paul, > > Galaxy manages output paths internally. The directory containing > datasets can be changed with 'file_path' in universe_wsgi.ini. By > default, it's database/files/ > > --nate > > > > -- > Paul Rigor > http://www.paulrigor.net/ > http://www.ics.uci.edu/~prigor > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

1 0

[hg] galaxy 2529: Use z-index:-1 instead of previous methods
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5003b7d10ff5 changeset: 2529:5003b7d10ff5 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:35:44 2009 -0400 description: Use z-index:-1 instead of previous methods 1 file(s) affected in this change: templates/base_panels.mako diffs (12 lines): diff -r 4ca7f95f854a -r 5003b7d10ff5 templates/base_panels.mako --- a/templates/base_panels.mako Mon Aug 03 17:23:52 2009 -0400 +++ b/templates/base_panels.mako Mon Aug 03 17:35:44 2009 -0400 @@ -125,7 +125,7 @@ </a> </div> - <div style="position: absolute; left: 200px; width: 60%; text-align: center"> + <div style="z-index: -1; position: absolute; left: 0px; width: 100%; text-align: center"> <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr>

1 0

[hg] galaxy 2528: Maintain centering
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4ca7f95f854a changeset: 2528:4ca7f95f854a user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:23:52 2009 -0400 description: Maintain centering 1 file(s) affected in this change: templates/base_panels.mako diffs (12 lines): diff -r 19b47949aa8a -r 4ca7f95f854a templates/base_panels.mako --- a/templates/base_panels.mako Mon Aug 03 17:19:04 2009 -0400 +++ b/templates/base_panels.mako Mon Aug 03 17:23:52 2009 -0400 @@ -125,7 +125,7 @@ </a> </div> - <div style="position: absolute; left: 200px; width: 500px;"> + <div style="position: absolute; left: 200px; width: 60%; text-align: center"> <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"> <tr>

1 0

[hg] galaxy 2527: Merging from central
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/19b47949aa8a changeset: 2527:19b47949aa8a user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 17:19:04 2009 -0400 description: Merging from central 0 file(s) affected in this change: diffs (truncated from 4323 to 3000 lines): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/datatypes/metadata.py Mon Aug 03 17:19:04 2009 -0400 @@ -497,7 +497,7 @@ return None def get_dataset_metadata_key( self, dataset ): return "%s_%d" % ( dataset.__class__.__name__, dataset.id ) #set meta can be called on library items and history items, need to make different keys for them, since ids can overlap - def setup_external_metadata( self, datasets, exec_dir = None, tmp_dir = None, dataset_files_path = None, output_fnames = None, kwds = {} ): + def setup_external_metadata( self, datasets, exec_dir = None, tmp_dir = None, dataset_files_path = None, output_fnames = None, config_root = None, datatypes_config = None, kwds = {} ): #fill in metadata_files_dict and return the command with args required to set metadata def __metadata_files_list_to_cmd_line( metadata_files ): def __get_filename_override(): @@ -515,6 +515,10 @@ tmp_dir = MetadataTempFile.tmp_dir if dataset_files_path is None: dataset_files_path = galaxy.model.Dataset.file_path + if config_root is None: + config_root = os.path.abspath( os.getcwd() ) + if datatypes_config is None: + datatypes_config = 'datatypes_conf.xml' metadata_files_list = [] for dataset in datasets: key = self.get_dataset_metadata_key( dataset ) @@ -547,7 +551,7 @@ metadata_files.flush() metadata_files_list.append( metadata_files ) #return command required to build - return "%s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) + return "%s %s %s %s %s %s" % ( os.path.join( exec_dir, 'set_metadata.sh' ), dataset_files_path, tmp_dir, config_root, datatypes_config, " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ) ) def external_metadata_set_successfully( self, dataset ): metadata_files = self.get_output_filenames_by_dataset( dataset ) diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Aug 03 17:19:04 2009 -0400 @@ -71,7 +71,7 @@ # add composite files name = composite_file.get( 'name', None ) if name is None: - log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) optional = composite_file.get( 'optional', False ) mimetype = composite_file.get( 'mimetype', None ) self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Mon Aug 03 17:19:04 2009 -0400 @@ -595,7 +595,7 @@ self.real_path = real_path self.false_path = false_path def __str__( self ): - if false_path is None: + if self.false_path is None: return self.real_path else: return self.false_path @@ -616,14 +616,18 @@ for outfile in [ str( o ) for o in output_paths ]: sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes - def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, **kwds ): + def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path if dataset_files_path is None: dataset_files_path = self.app.model.Dataset.file_path + if config_root is None: + config_root = self.app.config.root + if datatypes_config is None: + datatypes_config = self.app.config.datatypes_config job = model.Job.get( self.job_id ) - return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, **kwds ) + return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): def __init__( self, app ): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Aug 03 17:19:04 2009 -0400 @@ -13,7 +13,31 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + class HistoryListGrid( grids.Grid ): + # Custom column types + class DatasetsByStateColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + rval = [] + for state in ( 'ok', 'running', 'queued', 'error' ): + total = sum( 1 for d in history.active_datasets if d.state == state ) + if total: + rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) + else: + rval.append( '' ) + return rval + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + if history.deleted: + return "deleted" + elif history.users_shared_with: + return "shared" + return "" + def get_link( self, trans, grid, item ): + if item.users_shared_with: + return dict( operation="sharing", id=item.id ) + return None + # Grid definition title = "Stored histories" model_class = model.History default_sort_key = "-create_time" @@ -21,12 +45,8 @@ grids.GridColumn( "Name", key="name", link=( lambda item: iff( item.deleted, None, dict( operation="switch", id=item.id ) ) ), attach_popup=True ), - grids.GridColumn( "Datasets (by state)", method='_build_datasets_by_state', ncells=4 ), - grids.GridColumn( "Status", method='_build_status', - link=( lambda item: iff( item.users_shared_with, - dict( operation="sharing", id=item.id ), - None ) ), - attach_popup=False ), + DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), + StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Age", key="create_time", format=time_ago ), grids.GridColumn( "Last update", key="update_time", format=time_ago ), # Valid for filtering but invisible @@ -49,21 +69,6 @@ return trans.get_history() def apply_default_filter( self, trans, query ): return query.filter_by( user=trans.user, purged=False ) - def _build_datasets_by_state( self, trans, history ): - rval = [] - for state in ( 'ok', 'running', 'queued', 'error' ): - total = sum( 1 for d in history.active_datasets if d.state == state ) - if total: - rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) - else: - rval.append( '' ) - return rval - def _build_status( self, trans, history ): - if history.deleted: - return "deleted" - elif history.users_shared_with: - return "shared" - return "" class HistoryController( BaseController ): diff -r 692c384c1ca0 -r 19b47949aa8a lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 16:07:36 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Aug 03 17:19:04 2009 -0400 @@ -40,16 +40,9 @@ if column.key: if "f-" + column.key in kwargs: column_filter = kwargs.get( "f-" + column.key ) - if column_filter == "True": - filter_args[column.key] = True - elif column_filter == "False": - filter_args[column.key] = False - elif column_filter == "All": - del filter_args[column.key] + query = column.filter( query, column_filter, filter_args ) # Carry filter along to newly generated urls extra_url_args[ "f-" + column.key ] = column_filter - if filter_args: - query = query.filter_by( **filter_args ) # Process sort arguments sort_key = sort_order = None if 'sort' in kwargs: @@ -143,6 +136,26 @@ if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): + if self.link and self.link( item ): + return self.link( item ) + return None + def filter( self, query, column_filter, filter_args ): + """ + Must modify filter_args for carrying forward, and return query + (possibly filtered). + """ + if column_filter == "True": + filter_args[self.key] = True + query = query.filter_by( **{ self.key: True } ) + elif column_filter == "False": + filter_args[self.key] = False + query = query.filter_by( **{ self.key: False } ) + elif column_filter == "All": + del filter_args[self.key] + return query + + class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True ): diff -r 692c384c1ca0 -r 19b47949aa8a scripts/set_metadata.py --- a/scripts/set_metadata.py Mon Aug 03 16:07:36 2009 -0400 +++ b/scripts/set_metadata.py Mon Aug 03 17:19:04 2009 -0400 @@ -5,6 +5,9 @@ top level directly. """ + +import logging +logging.basicConfig() import os, sys, cPickle assert sys.version_info[:2] >= ( 2, 4 ) @@ -27,6 +30,12 @@ tmp_dir = sys.argv.pop( 1 ) galaxy.model.Dataset.file_path = file_path galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir + + # Set up datatypes registry + config_root = sys.argv.pop( 1 ) + datatypes_config = sys.argv.pop( 1 ) + galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) ) + for filenames in sys.argv[1:]: filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' ) try: diff -r 692c384c1ca0 -r 19b47949aa8a templates/history/grid.mako --- a/templates/history/grid.mako Mon Aug 03 16:07:36 2009 -0400 +++ b/templates/history/grid.mako Mon Aug 03 17:19:04 2009 -0400 @@ -137,8 +137,9 @@ %if column.visible: <% # Link - if column.link and column.link( item ): - href = url( **column.link( item ) ) + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) else: href = None # Value (coerced to list so we can loop) diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/2 +ACGCTCCTTTAAAATATC ++/2 +IIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_phiX_sanger_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_phiX_sanger_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759/1 +GGACTCAGATAGTAATCC ++/1 +II#IIIIIII$5+.(9II diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343 +AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG ++ +IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIHI""I""IIII"I"""""""IIIIIIHIIII""1III +@HWI-EAS91_1_30788AAXX:1:1:1578:331 +GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""II7I +@HWI-EAS91_1_30788AAXX:1:1:1647:512 +GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTAANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIGII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620 +GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTGCNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA ++ +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIIII""I""IIII"I"""""""IIII@4EIII:""I?E6 +@HWI-EAS91_1_30788AAXX:1:1:1599:330 +GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTGCNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIII<III@IIII""I""IIII"I"""""""@IIHI16IF51""I:A< +@HWI-EAS91_1_30788AAXX:1:1:1652:270 +GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTGANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6IIII""I""IIII"I"""""""IIIIIIIIIII""<D9I +@HWI-EAS91_1_30788AAXX:1:1:1746:351 +GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTTTNNANNATACNANNNNNNNAAACTAAAAAANNCAAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""BIIIH:7IIII""I0>I +@HWI-EAS91_1_30788AAXX:1:1:1582:633 +GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGGGNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIFIIIIIC3I""IIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534 +GAATCATNNAATCCGCTTGGTTTGACACTTTGGATTTNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""II.IIIICIII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324 +GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGCTNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05III""I""IIII"I"""""""II3II-/EIGI""A84; +@HWI-EAS91_1_30788AAXX:1:1:1749:466 +GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTAANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""ICIIIIIGII@""EI1: +@HWI-EAS91_1_30788AAXX:1:1:1629:446 +GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATGTNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIII?H<EII""I:I? +@HWI-EAS91_1_30788AAXX:1:1:1763:587 +GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGCTNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII"")II? +@HWI-EAS91_1_30788AAXX:1:1:1616:363 +GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGGANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIIII""I""IIII"I"""""""FI@7II1IIII""-III +@HWI-EAS91_1_30788AAXX:1:1:1768:715 +GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTTANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC ++ +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""I9F< +@HWI-EAS91_1_30788AAXX:1:1:1572:270 +GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCTCNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII":"""""""IIII5IIIBII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272 +GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGTGNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT ++ +III""""""IIIIIIIII""FI"IIII""II+ICIII""I""IIII"I"""""""IIIIIIIIGII""I;I@ +@HWI-EAS91_1_30788AAXX:1:1:1673:514 +GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCATANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1II""I""IIII"I"""""""II%I'$+ACI/""3(.I +@HWI-EAS91_1_30788AAXX:1:1:1634:330 +GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACATANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG ++ +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8IIII""I""IIII"I"""""""IIIEIIIII8I""@7>I \ No newline at end of file diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343/2 +CNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG ++/2 +I""I""IIII"I"""""""IIIIIIHIIII""1III +@HWI-EAS91_1_30788AAXX:1:1:1578:331/2 +CNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""II7I +@HWI-EAS91_1_30788AAXX:1:1:1647:512/2 +ANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA ++/2 +I""I""IIII"I"""""""IIIIIIIIGII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620/2 +CNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA ++/2 +I""I""IIII"I"""""""IIII@4EIII:""I?E6 +@HWI-EAS91_1_30788AAXX:1:1:1599:330/2 +CNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA ++/2 +I""I""IIII"I"""""""@IIHI16IF51""I:A< +@HWI-EAS91_1_30788AAXX:1:1:1652:270/2 +ANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""<D9I +@HWI-EAS91_1_30788AAXX:1:1:1746:351/2 +TNNANNATACNANNNNNNNAAACTAAAAAANNCAAA ++/2 +I""I""IIII"I"""""""BIIIH:7IIII""I0>I +@HWI-EAS91_1_30788AAXX:1:1:1582:633/2 +GNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT ++/2 +I""I""IIII"I"""""""IIFIIIIIC3I""IIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534/2 +TNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT ++/2 +I""I""IIII"I"""""""II.IIIICIII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324/2 +TNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA ++/2 +I""I""IIII"I"""""""II3II-/EIGI""A84; +@HWI-EAS91_1_30788AAXX:1:1:1749:466/2 +ANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC ++/2 +I""I""IIII"I"""""""ICIIIIIGII@""EI1: +@HWI-EAS91_1_30788AAXX:1:1:1629:446/2 +TNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG ++/2 +I""I""IIII"I"""""""IIIII?H<EII""I:I? +@HWI-EAS91_1_30788AAXX:1:1:1763:587/2 +TNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA ++/2 +I""I""IIII"I"""""""IIIIIIIIIII"")II? +@HWI-EAS91_1_30788AAXX:1:1:1616:363/2 +ANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT ++/2 +I""I""IIII"I"""""""FI@7II1IIII""-III +@HWI-EAS91_1_30788AAXX:1:1:1768:715/2 +ANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC ++/2 +I""I""IIII"I"""""""IIIIIIIIIII""I9F< +@HWI-EAS91_1_30788AAXX:1:1:1572:270/2 +CNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC ++/2 +I""I""IIII":"""""""IIII5IIIBII""IIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272/2 +GNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT ++/2 +I""I""IIII"I"""""""IIIIIIIIGII""I;I@ +@HWI-EAS91_1_30788AAXX:1:1:1673:514/2 +ANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC ++/2 +I""I""IIII"I"""""""II%I'$+ACI/""3(.I +@HWI-EAS91_1_30788AAXX:1:1:1634:330/2 +ANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG ++/2 +I""I""IIII"I"""""""IIIEIIIII8I""@7>I diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_sanger_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_sanger_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,76 @@ +@HWI-EAS91_1_30788AAXX:1:1:1761:343/1 +AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAA ++/1 +IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIH +@HWI-EAS91_1_30788AAXX:1:1:1578:331/1 +GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1647:512/1 +GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTA ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1570:620/1 +GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTG ++/1 +IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1599:330/1 +GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIII<III@III +@HWI-EAS91_1_30788AAXX:1:1:1652:270/1 +GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6III +@HWI-EAS91_1_30788AAXX:1:1:1746:351/1 +GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1582:633/1 +GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1598:534/1 +GAATCATNNAATCCGCTTGGTTTGACACTTTGGATT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1572:324/1 +GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGC ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05II +@HWI-EAS91_1_30788AAXX:1:1:1749:466/1 +GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTA ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1629:446/1 +GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1763:587/1 +GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGC ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1616:363/1 +GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIII +@HWI-EAS91_1_30788AAXX:1:1:1768:715/1 +GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTT ++/1 +IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1572:270/1 +GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII +@HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 +GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGT ++/1 +III""""""IIIIIIIII""FI"IIII""II+ICII +@HWI-EAS91_1_30788AAXX:1:1:1673:514/1 +GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCAT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1I +@HWI-EAS91_1_30788AAXX:1:1:1634:330/1 +GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACAT ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8III diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid_f.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid_f.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_solid_r.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_solid_r.fastq Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out0.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out0b.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out0b.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 4 * 0 0 * * 0 0 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out1.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,145 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +1831_573_1004 0 PHIX174 278 25 33M = 278 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +1831_573_1219 16 PHIX174 2202 37 33M = 2202 0 TGCAGTGGAATAGTCAGGTTAAATTTAATGTGA KJOOHX]KAP[]]MBQ\TUFO]QMFGG=CLZ]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1242 0 PHIX174 648 37 33M = 648 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) +1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +1831_573_1448 16 PHIX174 2563 25 33M = 2563 0 CTTCATTGCATTCAGATGGATACATCTGTCAAC :BMPX5.QUW6+R]RIOU]]]]]]]]WCTQS]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1490 0 PHIX174 1767 25 33M = 1767 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +1831_573_1647 16 PHIX174 1118 37 33M = 1118 0 GACTCCTTCGAGATGGACGCCGTTGGCGCTCTC XSU]YZSLKMZ]Y[]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1684 16 PHIX174 3696 37 33M = 3696 0 AGTGCTGAGGTTGACTTAGTTCATCAGCAAACG ]]]]V]]]]]]]]]]]]]]]]]]]]]U\]][TX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 +1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +1831_574_109 0 PHIX174 3729 37 33M = 3729 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGC VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_148 16 PHIX174 2369 37 33M = 2369 0 TAGGTTTTCTGCTTAGGAGTTTAATCATGTTTC XOQ[]]]TKWRCLJJZRR][]TWVGVZW]WZTQ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# +1831_574_243 0 PHIX174 2129 37 33M = 2129 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGC ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +1831_574_575 16 PHIX174 4006 37 33M = 4006 0 AATGTCACGCTGATTATTTTGACTTTGAGCGTA TMHGZ]UE<L]]]EM]K"&I]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_592 16 PHIX174 2950 37 33M = 2950 0 GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCA LLVSIV]]ZSPPSWNDIW\VOM[]]QANSCGKI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- +1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +1831_574_734 16 PHIX174 5263 25 33M = 5263 0 GAGAGATGAGATTGAGGCTGGGAAAAGTTACTG P]VXTGPLRN@KE=ALXC7ARL7;>;OKA/!!< XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_824 16 PHIX174 3997 37 33M = 3997 0 ACCCTTCTGAATGTCACGCTGATTATTTTGACT ]\MN]]U?I]]TAN]]ZGK][\RR]T@>M]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ +1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +1831_574_1194 0 PHIX174 1136 37 33M = 1136 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGT \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1204 16 PHIX174 1445 25 33M = 1445 0 CCTAATGAGCTTAATCAAGATGATGCTCGTTAT JGMO%.S]S>EW]V,=Y[]]PCU]]]X]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +1831_574_1591 16 PHIX174 5118 37 33M = 5118 0 AAGCTGTTCAGAATCAGAATGAGCCGCAACTTC MLII]]\K!7]ST][]]]OO]]]]]X]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1624 16 PHIX174 4058 37 33M = 4058 0 TATTGAGGCTTGTGGCATTTCTACTCTTTCTCA ?IM@DV]M?NRTK@JPXS?>ENI;=AML=7=M[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +1831_574_1903 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_574_1961 0 PHIX174 3555 25 33M = 3555 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTT TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_54 16 PHIX174 3587 37 33M = 3587 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCG ]]4/WZUDARYXKAL]]MR]]]]\]]VW]W]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +1831_575_197 16 PHIX174 4861 37 33M = 4861 0 GCTTGCAAAATACGTGGCCTTATGGTTACAGTA G.<]KNV]]RH@AIT]\SP\]]]Y[]]\RS\]P XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. +1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +1831_575_444 16 PHIX174 5098 37 33M = 5098 0 AGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAA ]Y0/[]]MM]]]VT]]]]]]]]QP]]]TS]]][ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +1831_575_569 0 PHIX174 5043 25 33M = 5043 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAA IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_622 0 PHIX174 2485 37 33M = 2485 0 GTTTTACAGACACCTAAAGCTACATCGTCAACG ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +1831_575_663 16 PHIX174 1554 25 33M = 1554 0 CGACTTCTACCACATCTATTGACATTATGGGTC !&V]]NIPV]]YUXWZWTYPW]]]]]ST]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& +1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# +1831_575_938 16 PHIX174 1133 37 33M = 1133 0 GACGCCGTTGGCGCTCTCCGTCTTTCTCCATTG XJFX]]WUY[]RKYXU]]]]]]]]\]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_970 16 PHIX174 232 37 33M = 232 0 GAGGAGAAGTGGCTTAATATGCTTGGCACGTTC Z]]]XU]]]]]]]]]]]]]]]\]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +1831_575_1138 0 PHIX174 1913 37 33M = 1913 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCT VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1157 16 PHIX174 3736 25 33M = 3736 0 AGCGGTATGGCTCTTCTCATATTGGCGCTACTG TX//[\]PQ]]]Z]]]]GN]]O!']]]]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1180 0 PHIX174 4169 37 33M = 4169 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGT ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +1831_575_1302 16 PHIX174 5202 37 33M = 5202 0 CTTACCAAGCTGGGTTACGACGCGACGCCGTTC ?AGG9<JL@57BI,!6828KG54AH<6B>;VYL XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1310 16 PHIX174 1612 37 33M = 1612 0 TACTGACCAAGAACGTGATTACTTCATGCAGCG [M!!N]]]]]]]OX]]]ZKW]]QQ][][RU]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1321 0 PHIX174 2664 37 33M = 2664 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGAC ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1373 16 PHIX174 4221 37 33M = 4221 0 TCTGACGTTCGTGATGAGTTTGTATCTGTTACT WGIZ]OHLR]]QU]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +1831_575_1436 0 PHIX174 3460 37 33M = 3460 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATA []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1442 0 PHIX174 3317 37 33M = 3317 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTC \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +1831_575_1500 16 PHIX174 4269 37 33M = 4269 0 GAATTGGCACAATGCTACAATGTGCTCCCCCAA ]]]LQ]ZZX]]]][[[[][VZ\][[]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1535 16 PHIX174 1225 37 33M = 1225 0 TCACGTTTATGGTGAACAGTGGATTAAGTTCAT Z\]]][Y][]]]]]]]W]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +1831_576_32 16 PHIX174 988 25 33M = 988 0 TTGAGGATAAATTATGTCTAATATTCAAACTGG !6\NX[\]YMP]]YM]]]]]VMPGDW\]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? +1831_576_86 16 PHIX174 2981 37 33M = 2981 0 CATGTCTAAATTGTTTGGAGGCGGTCAAAAAGC JDKTAEKORA;<GOTUPHGVRTZI?BAMUDCKR XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +1831_576_266 16 PHIX174 280 37 33M = 280 0 AGATATGAGTCACATTTTGTTCATGGTAGAGAT E4FXQMCG]]R<FZG5#.Z]SN]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_327 16 PHIX174 4517 37 33M = 4517 0 TACTATTCAGCGTTTGATGAATGCAATGCGACA \[]]]XQ\]]\X]]]]\Y]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( +1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +1831_576_519 16 PHIX174 1625 37 33M = 1625 0 CGTGATTACTTCATGCAGCGTTACCGTGATGTT KMPKLIVPELLS]XRY]]YWV]]NJY]]Y][SZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_603 16 PHIX174 1576 37 33M = 1576 0 CATTATGGGTCTGCAAGCTGCTTATGCTAATTT ZWU]]ZS\]]]TY]]]RQ]]]Y]]]]VZ]]\S] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_655 16 PHIX174 3292 37 33M = 3292 0 TTGCTGCTGCATTTCCTGAGCTTAATGCTTGGG :@O]QV]]]TK]]]73]]]TM]]]QI[]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### +1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +1831_576_815 0 PHIX174 5186 37 33M = 5186 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTA Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_882 0 PHIX174 5053 37 33M = 5053 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACT Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_898 0 PHIX174 518 37 33M = 518 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTG ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_923 0 PHIX174 1050 37 33M = 1050 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTC MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +1831_576_1131 16 PHIX174 4061 37 33M = 4061 0 TGAGGCTTGTGGCATTTCTACTCTTTCTCAATC WTLN]WUHL]]S<PZQUOYSFZ]][IUXX>>]M XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +1831_576_1289 16 PHIX174 1899 37 33M = 1899 0 TTCAGTACCTTAACGCTAAAGGTGCTTTGACTT NLU]YXTCQ]][JEJMSX]YRU]]][]]]\X]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +1831_576_1367 0 PHIX174 1839 37 33M = 1839 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTC ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1416 0 PHIX174 4522 37 33M = 4522 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +1831_576_1605 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +1831_576_1729 16 PHIX174 5194 37 33M = 5194 0 TAATCCAACTTACCAAGCTGGGTTACGACGCGA ]VDP]]][]]]]]]]]]]]]]]UW]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 +1831_576_1982 16 PHIX174 5024 37 33M = 5024 0 TAACAAAAAGTCAGATATGGACCTTGCTGCTAA TP\NU]]]W[]]]][]]]]]]]]]]]]]VU]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +1831_577_40 0 PHIX174 2772 25 33M = 2772 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGG JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 +1831_577_133 16 PHIX174 1714 37 33M = 1714 0 CATGCGCTCTAATCTCTGGGCATCTGGCTATGA &/BFXKGOZZEPOS]]]]]]PY]RN]YW]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +1831_577_281 16 PHIX174 4577 37 33M = 4577 0 TTTTGACACTCTCACGTTGGCTGACGACCGATT ]]OI]]]]]\ZY]]WTJS]]\[]]]]]]]\]]P XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_288 0 PHIX174 3201 25 33M = 3201 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGAT SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_322 16 PHIX174 458 37 33M = 458 0 TTCTGCCGTTTTGGATTTAACCGAAGATGATTT OIJWXWT]]WACVSEK5:RJSSRSPVZONR[]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_362 0 PHIX174 2153 37 33M = 2153 0 CTTATTCGCCACCATGATTATGACCAGTGTTTC ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_382 16 PHIX174 4686 37 33M = 4686 0 GGTCGCAAGGCTAATGATTCACACGCCGACTGC HMJXWWS<===S]NGHPXOE;GV]O;CTROUWT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_464 0 PHIX174 2126 25 33M = 2126 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATT ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_488 16 PHIX174 4948 37 33M = 4948 0 GGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG ]OTZ]]]]]][V]Z]YW]]]]]][UTT]Q?COU XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +1831_577_545 0 PHIX174 1711 37 33M = 1711 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTA ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 +1831_577_559 0 PHIX174 3840 25 33M = 3840 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAA ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 +1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +1831_577_637 0 PHIX174 4247 37 33M = 4247 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 +1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +1831_577_692 0 PHIX174 3905 37 33M = 3905 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTC WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out2.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,97 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +1378_11_329 69 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ +1378_11_329 133 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# +1378_17_1788 69 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### +1378_17_1788 133 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$###### +1378_25_2035 69 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% +1378_25_2035 133 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# +1378_28_770 69 * 0 0 * * 0 0 GGTTGGGAGTTGGCGCGCGTGGTT ###$##%%$####%#%$#%%#($$ +1378_28_770 133 * 0 0 * * 0 0 CTGCTATGCCGGCCGCCTGCCCCT %##(#$$#%$#$%###$%%$##$# +1378_33_1945 69 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG .6;?;55697>8779457986264 +1378_33_1945 133 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG +9;64287788752796/576352 +1378_34_789 69 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#& +1378_34_789 133 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$ +1378_35_263 69 * 0 0 * * 0 0 GGCGGGGGGGGGGGGGGGGGGGGG $%%&,)3/)%$-6'$&5&#$''5. +1378_35_263 133 * 0 0 * * 0 0 GGGCGGGGGGCGGCGGGGGGGGGG ),,#%'$)'-(%&%'%',%%&&(& +1378_43_186 69 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#' +1378_43_186 133 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$# +1378_51_1671 69 * 0 0 * * 0 0 GGTGTTGTTCGGATGTAGCGTGGG ##%$$####$########$##0## +1378_51_1671 133 * 0 0 * * 0 0 TGGGTAGGTGCGGCTCTTGCGGTC ##$#$%###%%#%#$##$$##### +1378_56_324 69 * 0 0 * * 0 0 GCTGGGTGATCTAAGGAATGTAAT #$#####$$$#$$$$##%###*(# +1378_56_324 133 * 0 0 * * 0 0 AGGCTTGGATTGTTGCGCTGACCT /+#**###%%##%#####$$$#$# +1378_56_773 69 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$ +1378_56_773 133 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$ +1378_62_2027 69 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&# +1378_62_2027 133 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'# +1378_62_2029 69 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%# +1378_62_2029 133 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$### +1378_67_1795 69 * 0 0 * * 0 0 CGTGCCAACGACCGTCCTACGGAG @@.?7@@@.@:@A<<>>=>70<@7 +1378_67_1795 133 * 0 0 * * 0 0 TAGTGGGCTAGTCCGGGATCTACC B@C2@@?;-@@1>'A@@91@.@1' +1378_68_466 69 * 0 0 * * 0 0 GTGTCATCTGAGGTAAAGCATTGT /##$09#$#.=$#$76+$%1'### +1378_68_466 133 * 0 0 * * 0 0 GTGATCGTCGGTGCCAGTCCCTGT #(%)+##$#$#%#+$%##$##### +1378_68_1692 69 * 0 0 * * 0 0 TGTTCGATTTAGGTCTTGCCTCGC ###%%$%%##%$#$##$###$$#$ +1378_68_1692 133 * 0 0 * * 0 0 GGTCTTCTGGGCACGGGCCAAGTT ###)%'&%##$###%#######$# +1378_80_664 69 * 0 0 * * 0 0 TGTCTGCGTTGTATCTCTGGTGTA %##%,%$$#&$$###$#$%##'%# +1378_80_664 133 * 0 0 * * 0 0 CTGCTTTGATCCCCGGTGGAGCAC 7#%###$$6#######$##$$$## +1378_85_1786 69 * 0 0 * * 0 0 CCCTAGGAGCGTATACCGGACGAG ,'&/%/@,&1,&'/)&,6&&1)(( +1378_85_1786 133 * 0 0 * * 0 0 ATACTATGTCGATCTGTAAAAAAA )&.)#3%(a)$&%-,2#&+.-%0&./ +1378_86_1011 69 * 0 0 * * 0 0 AGGCGATGGGATATTATTTTACTT :$###)%##$9$###1$$#$2### +1378_86_1011 133 * 0 0 * * 0 0 CTACGTTATTGCTCTGTTTGTCCT ######$%##$$$%###%#$#### +1378_86_1789 69 * 0 0 * * 0 0 GGCCAGGTACTAATAAATTCAACA 1.51/&%#'$,*?%#6&0$$5,20 +1378_86_1789 133 * 0 0 * * 0 0 CGAATATCCCCTGGTTTAGAAGTA 61?1;@/>@<=/(.7'(<5@=%$= +1378_91_1596 69 * 0 0 * * 0 0 GCTTTTTCATTCGGTGCCTTTGGA '>%/3%=()8'#.%?50$&5>%)% +1378_91_1596 133 * 0 0 * * 0 0 TTAGCGGTTGACTATCTGCTGACA *&+'#9'(%*'#//,&<),/)'*# +1378_94_1595 69 * 0 0 * * 0 0 GCGGGTTAACCCAGTACCTCTGGC ,8@6'>8<76>@@(->9)7'*941 +1378_94_1595 133 * 0 0 * * 0 0 CGTGCGACAGCCCATGTTTTCAGA -=..5,3826&*+.+#+#%%6;%# +1378_95_1039 69 * 0 0 * * 0 0 GTTCTGTGCCAGGTGAGGTACGGA &##,./#$&)6##+,'#$$0(##$ +1378_95_1039 133 * 0 0 * * 0 0 CGGCGTCCATCTTCGCCTTGAGAT $##.#$##$$#%$#$%%$###$)$ +1378_95_1767 69 * 0 0 * * 0 0 CTAATTGACCGGGCAAGCTATTAA ',,2'(10/>:=/7).3&%6&)&6 +1378_95_1767 133 * 0 0 * * 0 0 ACACGCACCATCTGGCGGCTAACC 86<65<4<C27/$5+#;-$+#2%$ +1378_96_1037 69 * 0 0 * * 0 0 CTGCTGGGCCATTTGACTTACTCA '$#+#(##-%5##+*&###-.$$$ +1378_96_1037 133 * 0 0 * * 0 0 ATCCCCCAAGATGCCTGTTGATTG $#$'##$$$#%$$#%###+##$#$ +1378_96_1764 69 * 0 0 * * 0 0 TCTTTGTAACCCACTTAGTATTTC 4='28>.@4881B807:822>%)1 +1378_96_1764 133 * 0 0 * * 0 0 TACACCGGAACCTTGCACTAAAGC 6-9'<#+81?+*<8-=69&6;*3) +1378_98_1574 69 * 0 0 * * 0 0 AGGCGAGTGTGGGGGTTGTTTGAG +%%$#)##%##$####%###$%$# +1378_98_1574 133 * 0 0 * * 0 0 GTTCTGCCGGTGTCTGTGGCGGGC $$#+&$$####%$$$###$%#%%# +1378_107_1647 69 * 0 0 * * 0 0 GGTCTGGTTCTATGTTGGTCGACT ###'$$#$$$(#%###(#$##$%# +1378_107_1647 133 * 0 0 * * 0 0 AGGCCTACTACGCGTCATTGATAG &#$$#$(.#%#$$####&$%##($ +1378_111_829 69 * 0 0 * * 0 0 GGTCTTCTATGGTGCTAAATTAGT $##'&###$##)#%($#$%#$'%# +1378_111_829 133 * 0 0 * * 0 0 TGCGGCACTTGCTTCTTCGTATTT %#%##%#$%#$#%###$$##&#$$ +1378_111_1900 69 * 0 0 * * 0 0 GCACGCCTTTGGGCTAAGCCGTAA )$)'#%$########$'#&%$#(# +1378_111_1900 133 * 0 0 * * 0 0 TCCCCTCGCTCGGCTCTGTGCTGT $&%*$#(#)##$#'##%(##$#$% +1378_112_1483 69 * 0 0 * * 0 0 TGGAGTGGTGTGTTTGCTGAGCCA #$#)#############$#%#%'% +1378_112_1483 133 * 0 0 * * 0 0 TGTCCAGCTATGCGGCTTCCTCCT %#$+#%#&#$#####%####%$## +1378_125_1287 69 * 0 0 * * 0 0 TGACGTGGGTTGTCCCGTGAGATT ##$%%#$###$##$$#&%##$(%% +1378_125_1287 133 * 0 0 * * 0 0 TGTCTCTGGGGGGCCTGGTTAGGT $##13$'%#$###$$###$$$#&# +1378_126_468 69 * 0 0 * * 0 0 AAAAAACGGGCCGGGCGGACTAGG @@B@@@>@2>1+?:92)>@8&&<+ +1378_126_468 133 * 0 0 * * 0 0 TCTCCTGATTAGACATATCTCCGT 7>@318?=,=8@49579?..7,7) +1378_127_664 69 * 0 0 * * 0 0 TCGCTTTGCCTATGTTTGTTCGGA #%$%#&##$%#%%###$$###)-' +1378_127_664 133 * 0 0 * * 0 0 AGAGGTTGGTGTCTTGTCGCAGCT ##'#$######$$%######$$$# +1378_129_463 69 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAA ,)&20%8'(&35-***1-2&+510 +1378_129_463 133 * 0 0 * * 0 0 CCTGTGGGCCAAGCCCAATGAAAG 8),,<6(--)<()5&.&/8+;.2+ +1378_129_875 69 * 0 0 * * 0 0 GACCTTTACGTATTGGGGGTTGGC ###)###+###$##$#&%##$,#$ +1378_129_875 133 * 0 0 * * 0 0 TTTCTATGGCTTACGCTGTCTGCC #$($##%####%$#$#####$### +1378_140_1251 69 * 0 0 * * 0 0 TTTCCTTCGTGTGCGTGCGGAGTG #%#%$##$$$######.$$$%#%( +1378_140_1251 133 * 0 0 * * 0 0 ATCCTAGCGCGGTGTCTTGGGGAC #$%1#$$$##$##$#$#$##$%$$ +1378_141_809 69 * 0 0 * * 0 0 TCTCGTGGTTTCTTTTTTATGTGT ##%)##$$#####%$#$#%%#'## +1378_141_809 133 * 0 0 * * 0 0 TGTCCTCCAGTGTCTGTTGGGTGT %&,-##$$#(%###$#$$'###'# +1378_144_983 69 * 0 0 * * 0 0 GTTCGTTCGTGGTGTACGAGGGTG #(#%#####($#%##$$#%##%#) +1378_144_983 133 * 0 0 * * 0 0 AGCGCCCGGTTGGTGCGGCTCGTC -$(&%*$#*#))#$$$#%%$#$## +1378_153_270 69 * 0 0 * * 0 0 GGCCGTGTGCGGGTGTAGATTGGA %$##($######&##$&$$$$%## +1378_153_270 133 * 0 0 * * 0 0 AGTCCTTGTCCCCTGGGTTTTCCC +''$#&%$%#$##&$$($#&#$$# +1378_155_1689 69 * 0 0 * * 0 0 CGCGTTCGGACAAAGCTAGCACCT @4@@=6=@@<4:@@681@@@.24. +1378_155_1689 133 * 0 0 * * 0 0 TTGGGAGGGAGAGAGACTAGACCG ?4@@4<<??<?-@4@=4<5<?:/> +1378_157_1580 69 * 0 0 * * 0 0 GGGATTGAAGGGATGTATGCTAGG #%$&%#$$'%$%#$##*#%$$$$# +1378_157_1580 133 * 0 0 * * 0 0 TGGGCCTCGGTGCCCTTGGTCTGT #%)$##'#$$$&#####%#$#$## +1378_161_317 69 * 0 0 * * 0 0 AATCCATACCCACAAAAGCAGGCC .&%','(@''?7//+&)+2.+)0) +1378_161_317 133 * 0 0 * * 0 0 TTGGCCGGCAACCCCGGTACCTAA 7<,<'@)@>.)2@/')'&(?/-<( +1378_177_735 69 * 0 0 * * 0 0 CGAGCCCTAAACCATGAGATCGGA @@B>@AC9@A<B8@=9>7@5)>,0 +1378_177_735 133 * 0 0 * * 0 0 AGTACGCCATGTATTTGCGACCAG =?@?C<88@=>:7>@55/.,416, +1378_181_1684 69 * 0 0 * * 0 0 TTTCTGTTGTGGTTTTGTTGGGGT $##'$%'##%##$%$#$$####$* +1378_181_1684 133 * 0 0 * * 0 0 CGACTCCCGCATTCACGGTCAAGT &*#,##$#&$*$$#$#$$$#%$## +1378_187_1407 69 * 0 0 * * 0 0 TTGGGTGAAATCTTGTCGAGTGGA ####&##$$###$#####%##%%) +1378_187_1407 133 * 0 0 * * 0 0 TGGCGTCCACTCGTGGGTCTATCG $#$'%#$%$%&$%#####$#$#%# +1378_203_721 69 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/. +1378_203_721 133 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2& +1378_206_2039 69 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05 +1378_206_2039 133 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out3.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,2 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/bwa_wrapper_out4.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out4.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,3 @@ +QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT +081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out1.fastqsanger Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +@081017-and-081020:1:1:1715:1759 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +++!+++++++!!!!!"+++++++!!!!)!%!!+!!%! diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out2.fastqsolexa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out2.fastqsolexa Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,8 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK diff -r 692c384c1ca0 -r 19b47949aa8a test-data/fastq_conv_out4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_conv_out4.fasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,4 @@ +>1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG +>1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out1.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out2.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_out3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out3.tabular Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_F3.csfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_F3.csfasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Fri Jan 23 21:37:16 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090124033450140 --name=0176_20090114_1_skmusc_cov_25_ --tag=F3 --minlength=25 --mask=1111111111111111111111111 --prefix=T /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1708/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_F3 +T0020112221222232212331223 +>1378_17_1788_F3 +T0321123231332130012112033 +>1378_25_2035_F3 +T0132123233223231301322223 +>1378_28_770_F3 +T0132130321122112113211113 +>1378_33_1945_F3 +T2222222222222222222222222 +>1378_34_789_F3 +T0032232213201212333201323 +>1378_35_263_F3 +T0222122222212212222222222 +>1378_43_186_F3 +T0030130233222012123323213 +>1378_51_1671_F3 +T0322230223212213133212231 +>1378_56_324_F3 +T0022133220332332121320113 +>1378_56_773_F3 +T2323123202231013303111103 +>1378_62_2027_F3 +T0133110120313213121323223 +>1378_62_2029_F3 +T0313222132313312223122323 +>1378_67_1795_F3 +T0302322213023112220313011 +>1378_68_466_F3 +T0232031231223211023111323 +>1378_68_1692_F3 +T0223133132221012221100233 +>1378_80_664_F3 +T2132133320311112232202101 +>1378_85_1786_F3 +T0030130323120313230000000 +>1378_86_1011_F3 +T0130123303321313233323113 +>1378_86_1789_F3 +T0120030311113223330200230 +>1378_91_1596_F3 +T3330212233201303132132010 +>1378_94_1595_F3 +T2123212010211103233331020 +>1378_95_1039_F3 +T0122123110313312113320203 +>1378_95_1767_F3 +T2010121011031322122130011 +>1378_96_1037_F3 +T0031111100203211323320332 +>1378_96_1764_F3 +T0301011220011332101300021 +>1378_98_1574_F3 +T0233132112232313232212221 +>1378_107_1647_F3 +T0022113013012123103320302 +>1378_111_829_F3 +T0321221013321331331230333 +>1378_111_1900_F3 +T0311113121312213132321323 +>1378_112_1483_F3 +T0323110213032122133113113 +>1378_125_1287_F3 +T0323131322222211322330223 +>1378_126_468_F3 +T2313113203302010303131123 +>1378_127_664_F3 +T0020223322323133231210213 +>1378_129_463_F3 +T3113232221100211100320002 +>1378_129_875_F3 +T0333130322133012132313211 +>1378_140_1251_F3 +T0031130212122323133222201 +>1378_141_809_F3 +T0323113110232313233222323 +>1378_144_983_F3 +T1021211122332232122131231 +>1378_153_270_F3 +T0023113323111132223333111 +>1378_155_1689_F3 +T0332220222020202013020112 +>1378_157_1580_F3 +T3322211312232111332231323 +>1378_161_317_F3 +T1332211221001111223011300 +>1378_177_735_F3 +T1023012110323033321201102 +>1378_181_1684_F3 +T0120131112103310122310023 +>1378_187_1407_F3 +T0322123110131232223130312 +>1378_203_721_F3 +T0113000300111022230000203 +>1378_206_2039_F3 +T1111111111111111111111111 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_F3_QV.qualsolid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_F3_QV.qualsolid Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Fri Jan 23 21:37:16 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090124033450140 --name=0176_20090114_1_skmusc_cov_25_ --tag=F3 --minlength=25 --mask=1111111111111111111111111 --prefix=T /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1708/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_F3 +7 4 2 2 10 6 2 2 2 2 2 2 2 4 2 2 2 3 2 3 2 2 3 7 2 +>1378_17_1788_F3 +6 2 6 2 3 3 2 3 2 2 2 4 4 2 2 3 3 3 3 2 2 2 2 2 2 +>1378_25_2035_F3 +9 2 4 2 6 2 2 3 2 3 2 2 5 4 2 4 3 3 3 4 2 4 2 6 2 +>1378_28_770_F3 +2 4 2 2 7 2 3 3 2 4 3 2 3 4 2 2 2 3 4 4 3 2 2 3 2 +>1378_33_1945_F3 +18 10 24 26 21 19 17 23 22 22 23 23 22 20 17 22 24 21 14 20 22 21 18 20 17 +>1378_34_789_F3 +2 2 3 2 2 4 2 3 2 2 3 5 3 2 4 2 2 3 2 2 3 2 2 2 3 +>1378_35_263_F3 +3 8 11 11 2 4 6 3 8 6 12 7 4 5 4 6 4 6 11 4 4 5 5 7 5 +>1378_43_186_F3 +2 2 3 7 19 4 3 2 2 2 2 2 2 2 2 3 2 3 2 2 2 3 3 3 2 +>1378_51_1671_F3 +2 2 2 3 2 3 4 2 2 2 4 4 2 4 2 3 2 2 3 3 2 2 2 2 2 +>1378_56_324_F3 +3 14 10 2 9 9 2 2 2 4 4 2 2 4 2 2 2 2 2 3 3 3 2 3 2 +>1378_56_773_F3 +9 5 4 2 4 2 2 4 4 2 2 2 2 2 5 2 3 4 2 2 3 4 2 2 3 +>1378_62_2027_F3 +9 7 2 5 5 3 2 2 3 3 2 3 4 2 4 3 3 3 2 3 2 2 2 6 2 +>1378_62_2029_F3 +4 3 4 3 3 2 2 2 2 3 2 2 3 3 2 8 2 2 4 4 2 3 2 2 2 +>1378_67_1795_F3 +33 33 31 34 17 31 31 30 26 12 31 31 16 29 6 32 31 31 24 16 31 13 31 16 6 +>1378_68_466_F3 +4 2 7 4 8 10 2 2 3 2 3 2 4 2 10 3 4 2 2 3 2 2 2 2 2 +>1378_68_1692_F3 +3 2 2 2 8 4 6 5 4 2 2 3 2 2 2 4 2 2 2 2 2 2 2 3 2 +>1378_80_664_F3 +8 22 2 4 2 2 2 3 3 21 2 2 2 2 2 2 2 3 2 2 3 3 3 2 2 +>1378_85_1786_F3 +6 8 5 13 8 2 18 4 31 3 5 4 12 11 17 2 5 10 13 12 4 15 5 13 14 +>1378_86_1011_F3 +2 2 2 2 2 2 2 3 4 2 2 3 3 3 4 2 2 2 4 2 3 2 2 2 2 +>1378_86_1789_F3 +31 21 16 30 16 26 31 14 29 31 27 28 14 7 13 22 6 7 27 20 31 28 4 3 28 +>1378_91_1596_F3 +4 9 5 10 6 2 24 6 7 4 9 6 2 14 14 11 5 27 8 11 14 8 6 9 2 +>1378_94_1595_F3 +8 12 28 13 13 20 11 18 23 17 21 5 9 10 13 10 2 10 2 4 4 21 26 4 2 +>1378_95_1039_F3 +2 3 2 2 13 2 3 2 2 3 3 2 4 3 2 3 4 4 3 2 2 2 3 8 3 +>1378_95_1767_F3 +12 23 21 27 21 20 27 19 27 34 17 22 14 3 20 10 2 26 12 3 10 2 17 4 3 +>1378_96_1037_F3 +2 3 2 3 6 2 2 3 3 3 2 4 3 3 2 4 2 2 2 10 2 2 3 2 3 +>1378_96_1764_F3 +29 21 12 24 6 27 2 10 23 16 30 10 9 27 23 12 28 21 24 5 21 26 9 18 8 +>1378_98_1574_F3 +2 3 3 2 10 5 3 3 2 2 2 2 4 3 3 3 2 2 2 3 4 2 4 4 2 +>1378_107_1647_F3 +2 5 2 3 3 2 3 7 13 2 4 2 3 3 2 2 2 2 5 3 4 2 2 7 3 +>1378_111_829_F3 +2 4 2 4 2 2 4 2 3 4 2 3 2 4 2 2 2 3 3 2 2 5 2 3 3 +>1378_111_1900_F3 +10 3 5 4 9 3 2 7 2 8 2 2 3 2 6 2 2 4 7 2 2 3 2 3 4 +>1378_112_1483_F3 +9 4 2 3 10 2 4 2 5 2 3 2 2 2 2 2 4 2 2 2 2 4 3 2 2 +>1378_125_1287_F3 +4 3 2 2 16 18 3 6 4 2 3 2 2 2 3 3 2 2 2 3 3 3 2 5 2 +>1378_126_468_F3 +23 22 29 31 18 16 23 30 28 11 28 23 31 19 24 20 22 24 30 13 13 22 11 22 8 +>1378_127_664_F3 +9 2 2 6 2 3 2 2 2 2 2 2 3 3 4 2 2 2 2 2 2 3 3 3 2 +>1378_129_463_F3 +4 23 8 11 11 27 21 7 12 12 8 27 7 8 20 5 13 5 14 23 10 26 13 17 10 +>1378_129_875_F3 +2 2 3 7 3 2 2 4 2 2 2 2 4 3 2 3 2 2 2 2 2 3 2 2 2 +>1378_140_1251_F3 +12 2 3 4 16 2 3 3 3 2 2 3 2 2 3 2 3 2 3 2 2 3 4 3 3 +>1378_141_809_F3 +7 4 5 11 12 2 2 3 3 2 7 4 2 2 2 3 2 3 3 6 2 2 2 6 2 +>1378_144_983_F3 +11 12 3 7 5 4 9 3 2 9 2 8 8 2 3 3 3 2 4 4 3 2 3 2 2 +>1378_153_270_F3 +8 10 6 6 3 2 5 4 3 4 2 3 2 2 5 3 3 7 3 2 5 2 3 3 2 +>1378_155_1689_F3 +31 30 19 31 31 19 27 27 30 30 27 30 12 31 19 31 28 19 27 20 27 30 25 14 29 +>1378_157_1580_F3 +3 2 4 8 3 2 2 6 2 3 3 3 5 2 2 2 2 2 4 2 3 2 3 2 2 +>1378_161_317_F3 +8 22 27 11 27 6 31 8 31 29 13 8 17 31 14 6 8 6 5 7 30 14 12 27 7 +>1378_177_735_F3 +31 28 30 31 30 34 27 23 23 31 28 29 25 22 29 31 20 20 14 13 11 19 16 21 11 +>1378_181_1684_F3 +13 5 9 2 11 2 2 3 2 5 3 9 3 3 2 3 2 3 3 3 2 4 3 2 2 +>1378_187_1407_F3 +2 3 2 3 6 4 2 3 4 3 4 5 3 4 2 2 2 2 2 3 2 3 2 4 2 +>1378_203_721_F3 +33 24 27 16 10 17 10 16 31 28 17 20 24 31 10 26 17 13 22 16 5 31 10 17 5 +>1378_206_2039_F3 +26 24 31 30 23 29 26 29 29 29 27 27 24 24 19 26 28 23 24 20 23 24 20 12 23 diff -r 692c384c1ca0 -r 19b47949aa8a test-data/s2fq_paired_R3.csfasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_paired_R3.csfasta Mon Aug 03 17:19:04 2009 -0400 @@ -0,0 +1,99 @@ +# Mon Jan 19 06:35:55 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/0176/0176_20090114_1/skmusc_cov_25/results.01/primary.20090119120505312 --name=0176_20090114_1_skmusc_cov_25_ --tag=R3 --minlength=25 --mask=1111111111111111111111111 --prefix=G /data/results/0176/0176_20090114_1/skmusc_cov_25/jobs/postPrimerSetPrimary.1512/rawseq +# Cwd: /home/pipeline +# Title: 0176_20090114_1_skmusc_cov_25_ +>1378_11_329_R3 +G2233123221122322232333222 +>1378_17_1788_R3 +G3322232203232332312331032 +>1378_25_2035_R3 +G2232123122220222321323122 +>1378_28_770_R3 +G2223322202332212121232233 +>1378_33_1945_R3 +G2222222222222222222222222 +>1378_34_789_R3 +G3222133212330232020223323 +>1378_35_263_R3 +G2221222222222222222222222 +>1378_43_186_R3 +G3213022233322233321223222 +>1378_51_1671_R3 +G2223233233122032302123222 +>1378_56_324_R3 +G3213222320313002200323003 +>1378_56_773_R3 +G1313223122333122220232200 +>1378_62_2027_R3 +G2233221132211321123213212 +>1378_62_2029_R3 +G2221223232322321221323212 +>1378_67_1795_R3 +G1123211001201123113012202 +>1378_68_466_R3 +G1232310313202230002103323 +>1378_68_1692_R3 +G3323312033302231332113121 +>1378_80_664_R3 +G2323132123323031313223230 +>1378_85_1786_R3 +G3111302202123030112201202 +>1378_86_1011_R3

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[hg] galaxy 2525: Typos in cron/README.txt
by Greg Von Kuster 04 Aug '09

04 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8dcf04f31def changeset: 2525:8dcf04f31def user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 03 13:25:47 2009 -0400 description: Typos in cron/README.txt 1 file(s) affected in this change: cron/README.txt diffs (13 lines): diff -r aabcc797c1da -r 8dcf04f31def cron/README.txt --- a/cron/README.txt Thu Jul 30 16:23:47 2009 -0400 +++ b/cron/README.txt Mon Aug 03 13:25:47 2009 -0400 @@ -9,7 +9,7 @@ two things. First, updateucsc.sh must be edited to point towards the root galaxy directory. At the top of the file there is a variable "GALAXY" that should be edited. Second, the updates come from UCSC -via their table browsers. While the tendancy is typically to run crob +via their table browsers. While the tendency is typically to run cron jobs late at night, UCSC, like most, tend to take down their servers at odd hours for maintenance. The update scripts for UCSC are not CPU -intensive, and should be scheduled durring normal hours. +intensive, and should be scheduled during normal hours.

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