details: http://www.bx.psu.edu/hg/galaxy/rev/0d5182c4870b changeset: 2531:0d5182c4870b user: Kelly Vincent <kpvincent@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 ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%�'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-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'$/?6@/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<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 ++ +@++,)/)?./)%<)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).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>($<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$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 -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%�'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-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'$/?6@/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<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 -+ -@++,)/)?./)%<)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).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>($<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$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%@$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@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%@$&%-,2#&+.-%0&./ -@1378_86_1011/1 -CTACGTTATTGCTCTGTTTGTCCT -+ -######$%##$$$%###%#$#### -@1378_86_1789/1 -CGAATATCCCCTGGTTTAGAAGTA -+ -61?1;@/>@<=/(.7'(<5@=%$= -@1378_91_1596/1 -TTAGCGGTTGACTATCTGCTGACA -+ -*&+'#9'(%*'#//,&<),/)'*# -@1378_94_1595/1 -CGTGCGACAGCCCATGTTTTCAGA -+ --=..5,3826&*+.+#+#%%6;%# -@1378_95_1039/1 -CGGCGTCCATCTTCGCCTTGAGAT -+ -$##.#$##$$#%$#$%%$###$)$ -@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> <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) --> - <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> -<!-- <test> +<!-- + <test> <param name="pairedSingle" value="single" /> <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" /> <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> - <output name="output1" file="s2fq_out1.tabular" /> + <output name="output1" file="s2fq_out1.fastqsanger" /> </test> --> <!-- testing framework does not deal with multiple outputs yet @@ -58,8 +59,8 @@ <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" /> <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" /> <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" /> - <output name="output1" file="s2fq_out2.tabular" /> - <output name="output2" file="s2fq_out3.tabular" /> + <output name="output1" file="s2fq_out2.fastqsanger" /> + <output name="output2" file="s2fq_out3.fastqsanger" /> </test> --> </tests>