[hg] galaxy 3468: First pass of the new lastz paired reads tool....

3 Mar 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/bb7c2b314e3e
changeset: 3468:bb7c2b314e3e
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Tue Mar 02 16:40:40 2010 -0500
description:
First pass of the new lastz paired reads tool.  Tool page help and info needs to be corrected for this version of the tool.

diffstat:

 test-data/lastz_paired_input2.fasta             |  703 ++++++++++++++++++++++
 test-data/lastz_paired_input3.fasta             |    2 +
 test-data/lastz_paired_input4.qual454           |  700 ++++++++++++++++++++++
 test-data/lastz_paired_out1.sam                 |    2 +
 tool_conf.xml.sample                            |    1 +
 tools/sr_mapping/lastz_paired_reads_wrapper.py  |  756 ++++++++++++++++++++++++
 tools/sr_mapping/lastz_paired_reads_wrapper.xml |  371 +++++++++++
 tools/sr_mapping/lastz_wrapper.xml              |    4 +-
 8 files changed, 2537 insertions(+), 2 deletions(-)

diffs (2583 lines):

diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input2.fasta

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input2.fasta	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,703 @@
+>F2YP0BU02IPIOC length=313 xy=3454_0058 region=2 run=R_2009_09_24_17_10_49_
+TTTTTCCTCACAAGCATCACCATTCTGACCTTTATTATGATAGATTTATTTTGTCAGTTC
+TTAAATATCCTATAAAGAGAATAATACAGCATGCACTCTTTTTGTCTAGCCTCTGTGCTC
+AGTGTAATGTCTATGGGAGTCATCCACGTTAAGTATGGCAATAGCTCATTCTTTTCCATT
+GCTGCATAGTATTCCATTCTATCAGTCTATCATGTTTTATTTATCCATTTTCCTGCTGCA
+GATCATTTGGGATCATTTCCAGCTTTTGGCAATTATGAAAAATCGTATAACTTCGTATAA
+TGTATGCTATACG
+>F2YP0BU02GASSR length=219 xy=2466_0953 region=2 run=R_2009_09_24_17_10_49_
+TAATGAATAAGCATGAAGACAAGATTAGAGAAGAATGAAGGAATGAACAAGCCTCCAAGA
+ATATGGCACTATGTGAAAGACCAATCTATGTTTGATTGGTATACTTCGAAAGTGATGAGG
+AGAATGGAACCAAGTTGGAAACACTCTTCAGCGTAATAACTTCGTATAGCATACATTATA
+CGAAGTTATACGAATCATTGTTGTCTCTCCTGGTGGCAG
+>F2YP0BU02HLXG3 length=220 xy=3003_0293 region=2 run=R_2009_09_24_17_10_49_
+TTCATTTCCTTTGCTGCTTTCCCTTCATCTCCTCAATCCACAAACCGTAATAACTTCGTA
+TAGCATACATTATACGAAGTTATACGATCCAATTTCCTAACTTCTAAAATGAGAATTAAT
+CCTAATGCACTGCTCACTTCCCAGCAAGGGACATTCACTTTTCCACAAGAGCTCTCTTTA
+CAAAGCAATTCAACAGCTAAGGCAATGAAGTCAGTCAGTA
+>F2YP0BU02GF6D7 length=134 xy=2527_1997 region=2 run=R_2009_09_24_17_10_49_
+GAGAAGCATCAAATTCAACTCCATATCTGAAGTCAAGCCGTAATAACTTCGTATAGCATA
+CATTATACGAAGTTATACGAGAATTTGTGGTTCCTAGTTCTCAGTGTAATACTCCTTCCA
+ATATATATGATAGG
+>F2YP0BU02G6NFT length=92 xy=2829_0151 region=2 run=R_2009_09_24_17_10_49_
+TCTTCTCTCTGCCATTCTGCCAGGCTCAGTCGTATAACTTCGTATAATGTATGCTATACG
+AAGTTATTACGTATATATATGTGTGTATATAT
+>F2YP0BU02GD65M length=129 xy=2504_3880 region=2 run=R_2009_09_24_17_10_49_
+TTTAATTGGTTGTCTGGCTTTCTTATTGATGTGTCGTAATAACTTCGTATAGCATACATT
+ATACGAAGTTATACGAACAAAACAATAAAGAGATTATAATGGAGCTGAAAATTACCTATT
+GCCTAGTGA
+>F2YP0BU02GW28F length=318 xy=2720_0525 region=2 run=R_2009_09_24_17_10_49_
+GGTTTGAGCCACTGTGCCTGGCCAATTTTCTATTTTGTAGAGACAGGGTCTCACCATGTT
+GCCCAGGTTACGTAATAACTTCGTATAGCATACATTATAAGAAGTTATACGACATGTCTG
+CCGAAAGCTCAGTGGCAGGGCGGAGAGGGCCTGGGGCTGCCTCGTGAGGTGCGAGGGGTT
+CTTGTGAAGGTGGGGAGGCCCAGGGTCAGGGCCTCCCAAGGTAATGCTGAAGGGGCTCTG
+CTTCCAGAAGGGCCTGGACAACCTCAGAGGTCAGGGTGTTGAGCCAGGGGGCTCACCTTC
+CTCTCCTGCCAAGGGGCT
+>F2YP0BU02HKJIX length=388 xy=2987_1095 region=2 run=R_2009_09_24_17_10_49_
+TTTTATTGTGACTTTTATAAATGGAGATCATTGGGTAAAACGTAATAACTTCGTATAGCA
+TACATTATACGAAGTTATACGAACAAAGATAAGGAAATGGCAGGAGTGTTGCAGAAAGCA
+GTGGTTTCTGAAGACACAGGTATAGGCAGATATGAAATACAGAGAAGAAATTTGAGCTGG
+CGCTTCCAAATAACTGTACTTCTTTAGTGGTAAGATATCCCAAGCTTTGATTTCTCATCT
+TATTCACTTTGTCAGGAAGAGACAAACAGGTGTGGGTGCTGGGCAGAGGGCTTGATCTCA
+TTTTGCAGAGAAAGTGTTTGGAGACTTTGAACTAAGCAAAGAGTAACAGGGAAAATAAGA
+TAAAAATGAAAAGGGTAATGATTCGGAG
+>F2YP0BU02H80VC length=67 xy=3266_0534 region=2 run=R_2009_09_24_17_10_49_
+CTATGTTGACTAGGCTGGTCTCGAACTCCTGGGCTCAAGCAGGCCTTGTGCCTCGGCCTC
+CACCTAC
+>F2YP0BU02IO6IM length=284 xy=3450_0684 region=2 run=R_2009_09_24_17_10_49_
+TTGAACGGAATCGAATGGAATCATCATGGGATGGAAACGAATGGAATCATCATCGAATGG
+CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGAATGGACTCGAATGGA
+ATCAACATCAAACGGAATCAAGCGGAATTATCGAATGGAATTGAAGAGAATCATCGAGTG
+GACTCGAATGGAATCATCTAATGGAATGGAATGGAATAATCTATGGACTCGAATGCAATC
+ATCATCGAATGGAATCGAATGGAATCATCGAATGGACTCGAATG
+>F2YP0BU02GU7ME length=113 xy=2698_3012 region=2 run=R_2009_09_24_17_10_49_
+CCATATCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGATATTCCAGTC
+CGTCATTAAAATTAGATAATTTACGCCTAATAATTATATGTATGTATTGAAGC
+>F2YP0BU02HYBDH length=366 xy=3144_0643 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTTATATTCAGGCCCGCAATGTATTGGATCGTATAACTTCGTATAATGTATGCTAT
+ACGAAGTTATTACGTTTAATTCGATGTTGTCCATGAGTTTTGTTTTTCTATTTAGTTGCT
+ATGTTTGTTTTAATGTAAGGCAAGATTAAAATATTACACTGTCACCGTTACTACCATCCT
+CCCCAAATCCCCCTGTATTAGCTACCTAGGCTTGCTGGGTAACAAATTGTCACAAATTTA
+TTAGCAAAAGAACACACACTTGCTATATCACTGCTCTGTAAGTCAGAAGCCCAGGTGGGC
+TCGACTGGGTTCTGCACTTAAGGTCTCACAAGATTGAAATCAAGACATCAGCTGAGCTGG
+GCTCTT
+>F2YP0BU02GS94E length=98 xy=2676_3052 region=2 run=R_2009_09_24_17_10_49_
+AGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCAGGCACTGAGGAATG
+GTGAGAGGCACTGGGAATGGTGAGGGCGACTGGGAAGT
+>F2YP0BU02GFM2N length=339 xy=2521_1533 region=2 run=R_2009_09_24_17_10_49_
+GGTTTAATTGCTCATTCAGTAGGTAGTAAACTGCAATTCAATCAAGCATGCTAAACCATT
+GAAAATGAATGCATTACCAAGTATGAATAACTTGTTCATAATTCATTGAGCCGGCCATAG
+GGCAGGCACAACTAAGAGGCATTTGGCAACCAAAGCAATGCAAGCTGGTTGTGAGGAGAA
+AGAAGCTAGGATGCCTAAGAACAGATAGAAGAGCCTACCAGCCACTGACTCAGGTACAGA
+GCTAGTCACTAAAGATGAATATTGGTCTGATGACTACCGTCCGTAATAACTTCGTATAGC
+ATACATTATACGAAGTTATACGAGACATGAACAGAAATG
+>F2YP0BU02H2R5T length=71 xy=3195_0127 region=2 run=R_2009_09_24_17_10_49_
+GCAGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGCCTCATTCTCTTT
+AAATGTAGACA
+>F2YP0BU02IENAS length=319 xy=3330_0738 region=2 run=R_2009_09_24_17_10_49_
+TTTGTATAAAGTGAGAGATAAGAATCCAGTCGTAATAACTTCGTATAGCATACATTATAC
+GAGGTTATACGATATTCTGTATAGAGGTGATGGCTCATATAATTCAGCTGTGATAGCCAT
+AATTTCCAAAATGACAGTAGGAAAATAATGTCTCATGGAGATAAAGGAAACTGACAATAA
+AAATGGAAGAAGTACAAAAACTGCCATGTAAAATAATTCCTGGAAAATTTTTGAAAGTTT
+TGCTGGAAAACTTTTTTGAAAGTTTTGCTGGAAAAGACTACATACTTCTCCAAAAGAAAA
+GTAAACTTCTAAGTGTTAT
+>F2YP0BU02HT2D7 length=41 xy=3095_3085 region=2 run=R_2009_09_24_17_10_49_
+ATGGAGGAGTTGGGAGGACACTGTCTTGTAAGTCTGCAAGT
+>F2YP0BU02H8REW length=269 xy=3263_0566 region=2 run=R_2009_09_24_17_10_49_
+TTGACCCTTGACCTTTAGCTTCCTTCTTCCTTAACCAGCAAACCTCCATGCCCTATGTCT
+CCTAAATGTCCTTCAAATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGA
+GAAAAGGTCTTTGTTACTCATGGCACAGAAAGAAGCATGAGCTTCATGTTTGCATCAGTT
+CTTCTTGCTCTCCAAATCCCAAAGTAGGCAAGGTGGAGGTAGGCCAAGGTAAATTCTGTG
+AATCCAGTGAGTTTATGACACAGCTGAGG
+>F2YP0BU02IAR6Y length=369 xy=3286_0680 region=2 run=R_2009_09_24_17_10_49_
+TTTTGCTGAGAAGCAAATGCCACACAATCAATAACTCGTAATAACTTCGTATAGCATACA
+TTATACGAAGTTATACGATGAGAAAGGGAAAATGGCTCCTGAGAGTCCACCCTTGTGGAC
+TGCTATACTTGTCTGGTAGGAAAATTAATTTCAGTTTCTATGAAGGCATTGAAGTTGTCA
+ATATTTATTTCAATATTATTAATAATAATGATGTTCCGACATCCTGAATTCCAAGTTTCC
+TGCCACTTAAACCAACTGGAAAACCACTGTTTTAGATGGCTTTTCTAAAAGCCCACCCCC
+ATCAACAAGATACCCAAGATAGAGGGACTTACATGAAACATTCACTGAATGCTCCCAGAT
+GGGTACAAG
+>F2YP0BU02I3TZY length=65 xy=3617_0268 region=2 run=R_2009_09_24_17_10_49_
+TGGAATGGAACGGAATGGAATGGAATGGAATCAACCCGAGTGCAGGGGAATGGAATGGAA
+TGGAA
+>F2YP0BU02JP6S8 length=265 xy=3871_2922 region=2 run=R_2009_09_24_17_10_49_
+TTTGATCCCTTTTCCCGCCATCTTCTATGGCAACTCTGGCATTTACACCTCACTTTATGT
+ACGCCATGGCTTTTTCCATACTTCGAGGAGCCATCGCAGTAATGAGTTCGTGTCATTTCC
+TGTGGTTTTCTCCAGGGTATTAAATCCTGTATTCTGGGAAAGCACTTTCAAATTGATTAA
+TTCTCCCATATTCAAGTTTATATTCCGTAATAACTTCGTATAGCATACATTATACGAAGT
+TATACGAAGTCATTGTGTGAACATT
+>F2YP0BU02IG2DL length=165 xy=3357_2999 region=2 run=R_2009_09_24_17_10_49_
+TTGTCATAATTTGTTACAGTAGTCACAGTAAGGTTATTCAATACTGTAATTACATTTAGA
+ATCAATAATAGTAATATATCCACAAACCACAAATATTGAAATTAATATGCCTCTAAATAT
+CGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCTA
+>F2YP0BU02I6OA8 length=121 xy=3649_1794 region=2 run=R_2009_09_24_17_10_49_
+TTGCAGATTGCACTGAGGATTAGAGACAACATAGAAGCGTAATAACTTCGTATAGCATAC
+ATTATACGAAGTTATACGATTGAGAGATGCCTGGGTGAATCACAGACGTGAGTGGTGGAC
+A
+>F2YP0BU02JHJNK length=351 xy=3773_1070 region=2 run=R_2009_09_24_17_10_49_
+TTTTTAAACCTGGAAAATACACCAAATTTCAATTAAAAATGAAAATGGAAAGATCAAACA
+AGACATAAATAGAATCAGAAAGAATAGGGTTCGTATAACTTCGTATAATGTATGCTATAC
+GAAGTTATTACGAGTAGAGTCTTTTATAAAAACATCGCAAGATGTGCGAGGAACTAAAAC
+ATACTAAGGGGGAAGGATTTTTAACTCGGCCCCAGCAAAAAGAACTCTGTGCCCCTCCAT
+GGCCCTGGATGGCGGATGAGAGAGGGGCTCGCCTGCTCACAGAGCCCTAAGGACGGCGCC
+TCCGTGGCTCGAGCTTGTCTAAAGGGACTTGGAAGGTGTCTGGTGAAAAGG
+>F2YP0BU02JWZQ1 length=307 xy=3949_0875 region=2 run=R_2009_09_24_17_10_49_
+GGTTGTGCTTGAATTGGACAGATCCAGTGAAACTAATCAAGTACCTACTATGTGCCAAGC
+ATTGTGTCAGATGCTCTCACATGCATTATCTTGGAATCGTATAACTTCGTATAATGTATG
+CTATACGAAGTTATTACGCAAGCGTGTATTAATGGTACTAATTTCTGTAGTGCTATGAAT
+AGAATCTTACTATTTTGTGTCTAGTCTTTTTGTTCAACATTTGCGTGTGAGATTCATCCA
+TGCTGTTGAACAAAGTTCCATGTCATTCATTTCCATCATTTTATAGTACATTGGGTGATT
+AAACCAC
+>F2YP0BU02G4WWP length=149 xy=2809_1031 region=2 run=R_2009_09_24_17_10_49_
+ATTAAGTGAATAGTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATA
+ATATCTACCATATTGAGCTATTTTAAGCAGTAAATGAATAAAATACGCAAAGTGCATAGC
+ACATGGTAGATAATAAAGGAAGCTATTTC
+>F2YP0BU02IDILN length=130 xy=3317_1241 region=2 run=R_2009_09_24_17_10_49_
+TTACATAGTTATAGTAATCAAACATTATGATGCTCACATAAAACAGATACATAGATCAAT
+GGAATATAATAGAATACCCAGAAATAAGCCTATGCATATACAGTCAACTAATTCTTGAAC
+AAGGCACACA
+>F2YP0BU02I80Y8 length=435 xy=3676_0930 region=2 run=R_2009_09_24_17_10_49_
+TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGGTCTCAA
+GTGATCCACCCACCTCGGACTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCTACTTC
+TTTCTTTAACCTTCAGCTCATGGATCCCCTACCCAGCAAGACTTCAGGGCCCTGATGGGT
+TAGATGCCCCACCTCTGCTCTTCCATAGTGTTCGTAATAACTTCGTATAGCATACATTAT
+ACGAAGTTATACGATAGAAAAGTGTGCCACCAAGAAAGACCTGCATTGGAAGGGCTAGAT
+GTGTGCTGCATATGCTGCATAGACCTTTACAGGGGAGTCTCTTTTCTCCTTCTTGCTTCC
+TTTGCACAGAATCACCATAGGATATCACAGGAGCTTGTGCAGTTGGACTGAGACCGCCAA
+GGCACACAGGGGATA
+>F2YP0BU02JWZ8I length=437 xy=3949_1504 region=2 run=R_2009_09_24_17_10_49_
+TTTTTGTCAAATAATAATTCTATTACCAGCTAAACTATCAATCATCGTATAACTTCGTAT
+AATGTATGCTATACGAAGTTATTACGTGCTAAAACATTCAGCACGCTCCTCCTCTCTGCA
+GCCCATAGCCCAGGTACCTTAGTGCAGGGTGGAGGAAGCCTTGGGCAACCTGCTCTGTGA
+TGAGCAACCTATTCTCCTAACAGCCCGAGCCTTCCACCGCCCTGAGGCCTTGAAGCACCT
+TGGGGATGGCCTTCCTGCCTCTGCCTGGGCCCTCGCTGCTTCTGTCTGGAACTTCTCCTC
+CCAGTCCACGAGAGATAGCTTGAATCTTGTCCTGAAGACAGGGCTACAATGTTGTTTCGT
+TTTTACATCTTTCCCTGAATATTCTTTCCTGAATGTATGGCTTCTTTGTCTCTGTGTCTT
+GTCACCTTATGTTGTAT
+>F2YP0BU02J14RD length=322 xy=4007_3079 region=2 run=R_2009_09_24_17_10_49_
+AATTTGGAATATATACACCATGGAATACTACACAGCCATAAAGAAATGAGATCATGACAT
+TTGTAGCAATGTGGATGTAACTAGAGTCCATTATCCTAAGCAAACTAACACTGGAACAGA
+ATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAAAATCAATTCCTCCTT
+TCTATTTGTGGGCCAAATGATTTCATTTAAGTCACTTAATTCTGACACTCAGTTTCCTGT
+AAACTGTAAACTCTAAAATGCAGATTACAATACTCATCTTGTCTACCCAGGTTATTGTGA
+AAATCAATGAATTAATATACGT
+>F2YP0BU02GCKL1 length=376 xy=2486_1735 region=2 run=R_2009_09_24_17_10_49_
+GTTTAAGTTCAGGTTCACATAAGAAATGGGTTTGAGTCTTCCACTGACCATATCATTAAG
+GAATGCAACAGCCATCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGT
+ATTTCTTATTGTCATCTTCAATACTTAGTATCTATAAATTATAAACACTTTTGGATTTTT
+GTGGGTTTTTTCTCTCAACTGGAAAGCAAATACAAATAATAACATCTTTAAACAGAATTA
+ATCTTTAGATGTAGTAGAAGAGAATGAAACAATTGGGTTTTGGGGTTTTTTTGTTTGTTT
+GTTTGTTTGTTTTGCTTTTTGTAAACAGAGTCTTACTCTGTCGCTCAGGCTGGAGTACAG
+TGGCTTGATCTCAGCT
+>F2YP0BU02HV3CE length=220 xy=3118_3420 region=2 run=R_2009_09_24_17_10_49_
+AACCAGAATGGTGGTTCATCAGGAAATTACAACAATTAACATAAGTGCTGCAAATCGTAT
+AACTTCGTATAATGTATGCTATACGAAGTTATTACGAGACTACATATGATATTACTTAGA
+AAAGACGCTGTGGAAGTCTAACTCACATTTAAATATACTAAGATTATTTCATTCTAAAAT
+AATGAAACCATTCAGTTCTTTATCTTAGAAGGACATGATA
+>F2YP0BU02J45XB length=51 xy=4042_1197 region=2 run=R_2009_09_24_17_10_49_
+CAAGGACTAATGTCCAGAATCTACAAGGAACTCAACAATCAGCAAGAACAA
+>F2YP0BU02FXSE6 length=214 xy=2318_0144 region=2 run=R_2009_09_24_17_10_49_
+GTTTTCACATTGTTGGTGGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTA
+CGAGACTGACACCTGGAGAAGTCCAGCCCTCTTGAAGGAAGGCAAACCTAAATCTTTTAA
+AATAGAAAAGCATCTTATTTTTAAAGGCTTCCAGAGACATCAAGTTCACAATTTTCCCCT
+AACTTACTGTTGGGAAACCTGTTAAAAATATACT
+>F2YP0BU02GA5V8 length=62 xy=2470_1542 region=2 run=R_2009_09_24_17_10_49_
+TCCATTTGAAGAATGATTTCCATTCGAGACCATTCGATGATTGCAGTCTGTCATTGACTA
+GG
+>F2YP0BU02HKT8Z length=297 xy=2990_2705 region=2 run=R_2009_09_24_17_10_49_
+TTTACTAATATTATCTCATTTAATACTCTCAACAAGCACACAATGTACGTATTTATTCTT
+TCATTTAATAAGTATTTATGAAATGCCCACTACTATTCACCCATGATATTCGTAATAACT
+TCGTATAGCATACATTATACGAAGTTATACGATTTTTCAAAAACAAAAGTCACATTTAGC
+AAAATATTCAGTACTGGTGATCTGGGTAAAGGGTACACGGGAATTCTTTGCACTATTCTT
+GCAATATTTCTGTAAGTTTGAAATTCATTCAGAATAAAAGAAAAAGATACTAGTGTT
+>F2YP0BU02G42KJ length=363 xy=2811_0177 region=2 run=R_2009_09_24_17_10_49_
+GTTTCCTTCTCCACACCAGCCCCTCTACACATCACAGGTGACTCTAAGCGTAATAACTTC
+GTATAGCATACATTATACGAAGTTATACGAGTCAAGAATGACTGTCAGCTTTGCATCTGG
+AGGAGCTGAGGGGATGATGGTGTCCTTGGCCGAGATGGCACAGCTTGGGGAGGGAACTTG
+TTTGAGGAAGAAAATCAAGAATTCTATTTCGGACAGGCTAAATTTGAGCTTCCTCCTGTA
+CATCCATGTGGGGATAATGAGTAGGCAGTTGGGTATGGGTGGCGGGGGGCGGGGGACGGG
+GAGTGAAGGGTTCGATTTGGAATTATGTGGCAATTAAAACCTCAAAGCTGGCTAAGATCA
+CCT
+>F2YP0BU02HD86B length=333 xy=2915_2657 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGTACTTTCAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCT
+CCTGACCTCGTGATTCACCTGTCTTGGCCTTCCAAAGTGCTGGGATTACAGGCATGAGCC
+GCTGCACCCTGCTGAGATTTTTATTTTTAAGAAATTATTTAAATGTTATGGTTGTGAATT
+GAGTTATCCCATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGCTAAGA
+ACTGTATTTGGGAGACTAGTGTTTATATTTGTAGGTAAGGAGGCACACTGGCTTTTGGAG
+TTGTGAGTTGTTGTGCTGATTCTTTCTCACGTG
+>F2YP0BU02F3YKL length=277 xy=2388_1331 region=2 run=R_2009_09_24_17_10_49_
+TTGGGCACTTGTCTCTTAGACACTTTCAAGTTACCTACTGGACAGGAGAGACCTCTTCTC
+TATAAAGTATCACACTTGGAGGCTTTTCAGGCACAGGACCATAGATTGTAATATTTTCCA
+TAGCAGTTGCCCAATTTTATCTGCGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGACCTCACATAGTGCAGTTTGGGTTGAGCGGAGGTGGCCAGTAATGGGGGCCCCTGG
+GACTCCTGGGACCTCTGTCTTCTTCTCCCTGGAAGAG
+>F2YP0BU02HLAR5 length=447 xy=2995_3651 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTGGTATTTTTAGTAGAGACGGGGTTTCACGGTGTTAGCCAAAATGGTCTCGATCT
+CCTGAGCTCATGATCCGCCCGCCCCAGCCTCCCAAAGTTCTGGGATTACAGGCGTGAGCC
+TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCCCCTACTGGTCTGTGG
+TTGTTTTTCTGTTGGCTGCAGCAGGCTGGCTGTGGTTTTTCNCTTGCCATGACAACTTCT
+AATTGCCATGTACAGTATGTTCAAAGTCAGGTAACTCCTTATTGTAAGCAAACTATGTAA
+CTGCCCAGAGCAGCACATATAAACCAGCCTAATGTGAAAAAAGAAGAAATAGGCCGGGCG
+CAGTAGTTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAAGC
+CAGGAAATCGAGACCATCCTGGCTAAC
+>F2YP0BU02GGSTZ length=300 xy=2534_2405 region=2 run=R_2009_09_24_17_10_49_
+TGGATGGACTCATCATCGAATGGATTCGAATGGAATCATCGAATAAATTGATTGAAATCA
+TCATCGAATGGAATCGATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGC
+GAATGCAATCATCATCGTATAGAATCGAATGGAATCATCGAATGGACTCGAATGGATTAA
+TCATTGAACGGAATCAAATGGAATCATCATCTAATGGAAACGAATGGAATCATCATCGAA
+TGGAAATGAAAAGAGTCATCATCTAATGGAATTGCATGGAATCATCATATAATGGAATCG
+>F2YP0BU02JARMH length=257 xy=3696_0199 region=2 run=R_2009_09_24_17_10_49_
+TTACATTTTGCTCTCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATTCT
+GGGATTATAGGCCTGAGCCACTCAGTCTGGCCAATAATAACAAATTTAATTATTTTAAAA
+GTATTACTGTATTTCAGTCTTCTTTCAGCCTACAATATGGTATTAAATGCCTTACATGGA
+GACATATAAAGGATTTTACCATAATAACCTTTAAAACAAAAGTGATTTCCTAGAATTATA
+GGACAGAAAAAGAATGT
+>F2YP0BU02F6FA3 length=174 xy=2416_1645 region=2 run=R_2009_09_24_17_10_49_
+TGTTTCTTTAATTCTTTGAAGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTAT
+TACGCTTCCACCAGTGTGCATGCTCAGATTTGAAGTGAGTGTACACTGTGCCCAGAGGCT
+GTCTATGATGCCCCAGTTGGTCTTTGCATTTACTCCAGGCACGCCTTGCACACC
+>F2YP0BU02IE523 length=281 xy=3336_0509 region=2 run=R_2009_09_24_17_10_49_
+TTCTTTCTTTCTTTCTTTGTAGAGATGAGGTCTCACTATGTTGCTCAGGCTGGTTTCAAA
+CTCCTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAAAATCATTCTA
+CAGCACAGGTCCTCCCAGGTCCATGACTTACTGAGTAGATAAATGTAGCCAATACATGAG
+AAATCAAGTTAAAACCTGTCCCTGCTGAGCCAGCAGTATCTATAGCTGGGGTACTACATA
+AGTGGATTCTGGGGAGCTTATTTAGAAAAAGACCCATGGCT
+>F2YP0BU02HZ814 length=271 xy=3166_0842 region=2 run=R_2009_09_24_17_10_49_
+TTTATAATAAAATGCAATTCCTTAAAATAATTCAATCGTATAACTTCGTATAATGTATGC
+TATACGAAGTTATTACGTGACAAATCACCAGTCGAGAACTGAGCACCTTGAAATTGTGAC
+CAAATGGAATACAAAAGGTTTTTATGGACGGCTCAAAGGTTTTCATGGTTATGCAAACCA
+CTGAAAATTAGCTAGTTCAAATATATTTGATGGTACAGAAAAATATTCCCTTCACCTAGC
+AAAATGAATATAACAAAATATGGCAATCTGG
+>F2YP0BU02F8YG5 length=285 xy=2445_1015 region=2 run=R_2009_09_24_17_10_49_
+TTGCATTACCCAGAATTGGCCACCAGGGTAGGCTAGAGTTCGTATAACTTCGTATAATGT
+ATGCTATACGAAGTTATTACGCTCTTTGTTGATCCTAAAAGAAAATGGCAAGAATTTAAA
+GTGGTTTTGGATTGACAGTACCACCAAGAACCCAGCAGAAGCAATGCAGATCCTTTCTGG
+ATGAACTCATCTTTAATCTAGGCCTCGGGGAATTTCCACAGATACAGTTCCAAGAAAATA
+AATTGTGGTCAAAAATTCCAAACAAATAAGGAACGAGGCACCAAG
+>F2YP0BU02GJK8J length=290 xy=2566_1457 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTCTTCTTAATAACTGAAGAGAATAACATTTATCAAACAAACGATCGAACTCTTTC
+TGAGACATAGTTTCATGTGCCTCTTTGGAGTTGATTTCCCCTCCGTAATAACTTCGTATA
+GCATACATTATACGAAGTTATACGAGTGGCCATCAGGACATTTATTAGCTGTTAATCTAA
+CCACTACCAAATGCATTAACACATTTTTTTTGACAACTTTTTCTCTTTTATTTGGCTGTT
+GCTTAGTTCAGTTTTGCTTGGAGAAGTTGTGGCAATCCTGAATTCAGTTT
+>F2YP0BU02IFF38 length=137 xy=3339_1222 region=2 run=R_2009_09_24_17_10_49_
+TTGAGAATCAAATTTCACCATTAGTTTCTGAGGGAATCGTATAACTTCGTATAATGTATG
+CTATACGAAGTTATTACGGTCAAAATAAAAAGAAAATATAGGAAGAACAGGTAAAGAATG
+GTGAAAAATATCATTGT
+>F2YP0BU02JGYZX length=265 xy=3766_2971 region=2 run=R_2009_09_24_17_10_49_
+ATTTGAGTCCATTTGATGATTGTTCCATTCGATTCTATTCGGTGATTCCATTCGATTCCA
+TTTGATAATGATTCCAATCGAGACCATTCGATGATTCCATTCAATTCCATTCAATAATGA
+TCCCTTTCGTAGTCCATTCAATGATTCCTTTCCAGTCCATTCGATGATTCCATCTGATTC
+CATTCAATGAATCCCATTCGATTCGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGACATTCGATTCCATTTGTATG
+>F2YP0BU02JT6YF length=104 xy=3917_1317 region=2 run=R_2009_09_24_17_10_49_
+TTCCTAGGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGACCTGCTC
+AATTTAGATTCCACTTCCAGGAGTATGAGGATCTTCTCCTGGGA
+>F2YP0BU02FL7V0 length=282 xy=2186_0990 region=2 run=R_2009_09_24_17_10_49_
+TTCCCCAAACAGACCCTAGAATAGTCTTCCTTGGAAATTCCATGAGCAAATAGCGTAATA
+ACTTCGTATAGCATACATTATACGAAGTTATACGAGTCTGTTTTAGATAAATGATGTTCA
+GTGGACCTTTCTGTGATGGTGGAAATATTCTATATTTGTGCCATTCAATACAGTAGCCAC
+TAGACTATTGGTCTATTTGCACTTGAAATGTGGCTAATGAGACTCACAAATACAATTTTA
+AATTAATTTAATTTAACTTTAAATAACAACACGTATTTTATT
+>F2YP0BU02JF57F length=249 xy=3757_2521 region=2 run=R_2009_09_24_17_10_49_
+CTATCTACAAGTGAATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTAA
+CTTAAGAAAACACTCCACCATTAGACAAACAAAGGCACCAGAATGCAATGAACTATAATA
+CTTTACCCATTAGGTGAGTAAGAGCCAGTAAATCAAAGGGCTTTTAAAAACACAATTCCT
+CAGCTAACACCATGAAGCAAAATTAACCATATTAGTTCTCTTCAATTTTACACTTTTGGG
+GTTAGGTAC
+>F2YP0BU02IADK7 length=500 xy=3281_2233 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGAGATGGAGTCTCACTCCGTAGCCCAAGCTGGAGCGCAGTGGCATGATCTTGG
+CTCACTGCAACTTTGCCTCTTGGGCTCAAGTGATTCTCCTGCCTCAGCATCCCAAGTAGC
+TGGGACTACAGGAATGCACCACCACACCCAGTTAATTTTTTTGTATTTTTACTAGAGACG
+GGGTTCCACCATGTTGCCCTGGGTGGTCTTGAACTCTTGAGCTCAGACGATCCACCTGCC
+TTGGCCTCCTAAAATGCTGGGATTACAGGCATGAGCCACCATGCCCAGCCATTAAGTGGT
+ATTTCTACGTTTGCATGGCATGTGACTAAATTGATCAATATTCAATATCATGAAGGTGTG
+TGTTTGCATAATGTTGACCGGATCTAATAGGCAAACAAAGGGATATGTGAACAGAGTTCA
+AATGTATTTTAAAGATATTACCGTAATAACTTCGTATAGCATACATTATACGAAGTTATA
+CGAGCCACATTATTATTCTA
+>F2YP0BU02H62VV length=305 xy=3243_4041 region=2 run=R_2009_09_24_17_10_49_
+CTTAGATCACAACACCTAAGTCCTTTTGAATAACTGGAAGCCTTCGCAAGAAGGACAGGT
+ACAAAGAAGCTCAGACTGTAAGAACTACAGTAAATACCGAACTCTTCAAATCCCAGGAAC
+AGATAAACATCCACAAGCATCAAGACCATCTAGGAAAACATGACCTCATTAAATGAACTA
+AATATGGCACCAGGGACCAAACCTGGAGAAACAGAGATATGTGACCTTTCAGACCGTAAT
+AACTTCGTATAGCATACATTATACGAAGTTATACGAGAACATCATGGGTCTTCTAAGTAT
+GTCAC
+>F2YP0BU02GQK0T length=370 xy=2646_0091 region=2 run=R_2009_09_24_17_10_49_
+AGTGTTCTCCTTCATGAATGAATGGTTCCATCTATGTCTGCTCTATCTCAGTCGCCAGAA
+TAATGAATCAAAGAATAATTAAGCCTATTAATAAAATGGTCAATTTATTTTAATTTATTG
+GCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGGCACAGAAAGACAAAT
+ATTGCATGTTCTGACTCTTGTGTAGGAACTAAAAGGTTGAATTCATTGAGATAGAGTAGA
+ATGATAGATACCAGAGGCTGGGAAAGGTATGTGGGTGGGCAAAATGAAGAGAGGTAGGTT
+AATAGGCACAAACAGGAAGTTATTTGGAAGGAGCAAGTTCTAATGGTTGATAGCAGAGTG
+GGTGATTAAG
+>F2YP0BU02JPJK8 length=198 xy=3864_1498 region=2 run=R_2009_09_24_17_10_49_
+CACAGTACCATGTCACACTGGCATTGCCTGAATCATTGCCTGAATTCAGCATAGCCTCTG
+CGCACCAGGTACTGTTCCAGGTGTCAGGGATATTGTGGTGAACAGGACAGACAAGGTCCA
+GGCCTCGTGGGGTTACGATTCTGGTGGGAGCGTATAACTTCGTATAGCATACATTATACG
+TAAGTTATACGATCTTTA
+>F2YP0BU02JYTJJ length=335 xy=3970_0125 region=2 run=R_2009_09_24_17_10_49_
+GTTTATCTTTCTTCTCATTCCATTTAAGGTCAATCTTTCCTCTAGTGCTCTTCATCCTAT
+CCCCACTTCCCTTCTTATCTAAACTCTTGTCTAGGAAATCTCATTAGCTCCTTTGGCTTT
+AACTACTAACTGATTACCTTCAGCTCAGTACTCCTGAGGAATATATCCCCACTCGTATAA
+CTTCGTATAATGTATGCTATACGAAGTTATTACGTAAAACAGCTAGGTGTTTCTGCTAAG
+AAACACTGCGTGGTAACGTTTCCCGGATAGCCCCAAAATGATCTCTATCTTCTGGTGTTT
+ACACCATGTGTAGTCCCTTCTCACAATATACATAC
+>F2YP0BU02GWFAR length=384 xy=2712_2273 region=2 run=R_2009_09_24_17_10_49_
+TTCTAAGATAGAAGTTTAGATAATTAATTTTGTAACTTTATTCTTTTAAATACATGCACT
+AAATGTTACAAATTTCCCTCTACACACTGCTTTTGCTGCAGACTACAAATTTTAATTAAT
+ATATTTTTATTTTATTGATTATTATTATTATTTAACGACAGGGTCTTGCTCTGTCACCAG
+GCTGGAAGGCAAGTAATACAATCATAGCTCGTATAACTTCGTATAATGTATGCTATACGA
+AGTTATTACGAATCCTTTGGGTATGTACCCGTGATGGGATGGCTGGAACAAATGGTTATT
+TCTAGTTCTAGACCCTTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTA
+CAGTCCCACCAACAGTGGAAAAGT
+>F2YP0BU02JXVRY length=55 xy=3959_1420 region=2 run=R_2009_09_24_17_10_49_
+TTACCCTTCTGTATAATGGAGATGGCTTATTTTCTCAAACCTCATGAACTACCCC
+>F2YP0BU02JWAD0 length=227 xy=3941_0774 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTAACCAAAGGACTAAAGTCATAGGAAGAAAAGCATACACTGGTTTTCTGGA
+CATTCCCCTGGGATTATACACACACACCATGCAACAATCACAGGCACCAGCTCCCAGCAG
+GCACATTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTGCAGCCCAGCC
+AGGGGCGGAGGAAGGCAGGAGTGGGGTCTGCAGCTGTCACCCGGAGC
+>F2YP0BU02GX9F0 length=48 xy=2733_1982 region=2 run=R_2009_09_24_17_10_49_
+AGTTCCGTGAGGACAGGACTATACAGTCAGCCCTCAGTATCCATGGGG
+>F2YP0BU02GRICP length=451 xy=2656_2327 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTTTTTTGGTAGAGACAGGGTTTTGCTGTGTTGCCCAGGCTGGTCTCAAACT
+CCTAAACTTAAGTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTATAGGTGAGAG
+CCACTGCGCCCAGCTCACGATTGTTAAATCTAAGGGCTCTGAAAATAGCAAGTTTTTGTA
+TAATTGTTTCAATGGCAAGACCTGGCCTGGACTGATGTGAAGCCGCTGGTTGTTGTTATT
+CCATCACTTCAGCTGCAGAAATACTGTGTTTATTGTGGGGGCTGCCCAGACCTGTGGGTG
+GCACTAGATAATCGACAGGAGCTCCCCTTGTAGCGTAATAACTTCGTATAGCATACATTA
+TACGAAGTTATACGATATGTGTACCTACTATTTTGGGACACAAGGGTATTAAAAACCATG
+TACTCAAGGGCTGATATTTAATAAAATTAAT
+>F2YP0BU02GIUVR length=132 xy=2558_0069 region=2 run=R_2009_09_24_17_10_49_
+ATTAGGCTGATACTACCTGAATCCAGCTTAAGACATAAAGTCATTATGTCGTAATAACTT
+CGTATAGCATACATTATACGAAGTTATACGATTGAAGGTCACCAAACCAAATCATAACAA
+TCTTCCTCAAAT
+>F2YP0BU02FJD9A length=189 xy=2154_0348 region=2 run=R_2009_09_24_17_10_49_
+AAAAGAACATGAGTTTCCAGAGCCTGGTGGCCTGGGTTAGAATCCTAGCTCTGCAACTCA
+TGGCTGTGTACTATTTGGCCAAGTAACTTAACCTTTCTGTGCTTTAGTTTCCTCATCTCT
+AAAATATGTATCTTTTTNTTTTCCCTTTCGAGACAAGAGTCTCACTGTGTCACCTCGTAT
+AACTTACGT
+>F2YP0BU02IIGW9 length=372 xy=3373_2971 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTTATATTCAGGCCCGCAATGTATTGGATCGTATAACTTCGTATAATGTATGCTAT
+ACGAAGTTATTACGTTTAATTCGATGTTGTCCATGAGTTTTGTTTTTCTATTTAGTTGCT
+ATGTTTGTTTTAATTGTAAGGCAAGATTAAAATATTACACTGTCACCGTTACTACCATCC
+TCCCCAAATCCCCTCGTATTAGCTACCTAGGCTTGCTGGGTAACAAATTGTCACAAATTT
+ATTAGCAAAAGAACACACACTTGCTATATCACTGCTCTGTAAGTCAGAAGGCCAGGTGGG
+GCTCGACTGGGTTCTGCACTTAAGGTCTCACAAGATTGAAATCAAGACATCAGCTGAGCT
+GGGCTCTTATCT
+>F2YP0BU02JF0IJ length=54 xy=3755_3337 region=2 run=R_2009_09_24_17_10_49_
+AATAATAATATCATGTCCACAGTGGAGGTCTACAGGAACAAAGGAAAGAATAAA
+>F2YP0BU02HU4M2 length=275 xy=3107_3500 region=2 run=R_2009_09_24_17_10_49_
+TGCCTGTAAATAGGAATAATTCTAATAGTAACTCTCGTATAACTTCGTATAATGTATGCT
+ATACGAAGTTATTACGAGCACATAAAGATGAGGATTTAATTTTAGTATTAATGATCTCAA
+AGCTGGTTAATGTCTGACAATGAGCAGATACATGATGCAGGTATACTTCATGAATTTGTC
+TCATTTCTTGTTAGAAGCTGCTAGACTCAGTGAGCTTTAATTTGCTGAGACTGACAAAAT
+AGCAGATTTTCACTGAACCTGACTAGCTGGTTTTC
+>F2YP0BU02H8Z84 length=68 xy=3265_3830 region=2 run=R_2009_09_24_17_10_49_
+TTATTTGTTGCATTTATATGTGGGTAGATCAATAACTTAATTTCTATAGAACAATATTCT
+TTTGTTTG
+>F2YP0BU02F2LFK length=373 xy=2372_3182 region=2 run=R_2009_09_24_17_10_49_
+TTTCCTTTTCACCATAGGCCTGAAGCGATCCAAATGTCCACATCCAGATACTACAAAAGA
+GTGTTTCAAACCTGCTCTATGAAAGGGAATGTTCAACTCTGTGACTTGAATGCAAACATC
+ACAAAGAAGTTTCTGAGAATGCTGCTGTCTGCTTTTTGTATGTAATCCCGTTTCCAACGA
+AATCCTCCCAGCTAGCCAAAATATCCACTTGCAGATTCCGCAAAAAAGAGTGTTTCAAAA
+CTGCTCCTTCAAAACGATGGTTTAGTTCTGTTAGTTGAGTACATACATCTCGTATAACTT
+CGTATAATGTATGCTATACGAAGTTATTACGTATCCACTTGCAGATTCCACGAAAACAGT
+GTTTCAAAAACTG
+>F2YP0BU02HCBFV length=56 xy=2893_2393 region=2 run=R_2009_09_24_17_10_49_
+TTTATGAAACAAAGGAACTTGTCATAGTCTATTAAAGCAATCTCCTAACCCCACTG
+>F2YP0BU02GR0SM length=100 xy=2662_1652 region=2 run=R_2009_09_24_17_10_49_
+TGTTTCTCCATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTCCAGCAA
+GGTATTTCGATAGGAACTGTGATAATACCAGCCCTCATAG
+>F2YP0BU02GN26J length=416 xy=2617_2441 region=2 run=R_2009_09_24_17_10_49_
+GGTTTATATGTACCATGTTTTATTTATCCCATCCGCTGTTCATGGGCACATAGGTTGATT
+GATTCCATGTCTTTGCTATTTTGAATAGCACTGCAGTGAACATATGGGTGCATGTGTCTT
+TTGGATAAACGAATTATTTTCTTTGGGTATATATCCAGAAGTGGGATTCCTGGTTTAAAA
+TGGTAATTCCATTTTTAAGTTCTTTGAGAAATCTCCAGACTCGTAATAACTTCGTATAGC
+ATACATTATACGAAGTTATACGATTATCTGTATTACAGGGAATAATGTGATATTGGAGTT
+ACTATGTCCATTATGTTTTAAAGCTTTTTCTCAGTTTTAGTACTTTAAGATGACATAAGT
+TGTGTCATCCTTGAATGTGTTGGCTATTGCATGAAAAGACCCTATATTTACTTTTG
+>F2YP0BU02HGJBL length=377 xy=2941_2623 region=2 run=R_2009_09_24_17_10_49_
+TTACAGGCATGAGCCACCGCACCCAGCCTCTATTTCCTTTTAAAATTGAATGCCTTTAAC
+AGCACCCAAGTCACCTCTTGAATGTTGTATTGCTTAGAAATTTCATCCGCCAGATACCCT
+AAATCATCTCTCTGAAGTTCAAATTTCCACAAACCTCCAGGGCAGGGGCAACATGCCACC
+AATCTTTTGCTAAAACAAGTTATAGCAAACAACTTCCTCCGTAATAACTTCGTATAGCAT
+ACATTATACGAAGTTATACGATGATAATGGTAGTTGATAATGGCAGTTCATGGGTGAAGT
+TGCTCAGGAAGAATGAATATACTGTGAGACAAAATGACCACTACTGTTTGAGAGCTACGT
+TGAAGAAGGGGAGCCTG
+>F2YP0BU02HEDVO length=61 xy=2917_0562 region=2 run=R_2009_09_24_17_10_49_
+TAAGCCACTCACACTCCTCCAAAGGCAGTCAGAGCTCCTTCAGCTTGCCCACCTACTCTC
+T
+>F2YP0BU02II7P9 length=196 xy=3382_0847 region=2 run=R_2009_09_24_17_10_49_
+ACAGTGAGACTCTGTCTCAAAGAAAGAGAAGAGGCCTGGTGCAGAGGCTCACGCCTGTAA
+GCACTTTGGGCGGCCGAGGTAGGCGGACCACTTGAGGTCAGGAGTTCTAGACCAGCCTGG
+GCAACATGGCAAGATCCCATCTCTAATAAAATCGTATAACTTCGTATAATGTATGCTATA
+CGAAGTTATTACGTAA
+>F2YP0BU02IDY8I length=200 xy=3322_2320 region=2 run=R_2009_09_24_17_10_49_
+TTTAAAATGTCTATTAGCAGTGATGTTTGAACTAGTCTTTTGAGAAGTGTGAAGAGAACA
+GGAAAAGTCTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTATACAC
+ATTTCGGGGCTGAGAGGCTAAAATGAGAATGGCGCAGCGGACGGGGAAGGCTTCTCTGCA
+CACAGCTGCTGGGATCTGAG
+>F2YP0BU02GLX2B length=189 xy=2593_0801 region=2 run=R_2009_09_24_17_10_49_
+AGTAATAAATAAAATCAAGGCTGGGGAATTACTACCAAGCTAAGCTCTGAAATCCAAAGC
+AAGAATTTAATATTTCCATTTTTCTGGCCGTAATAACTTCGTATAGCATACATTATACGA
+AGTTATACGATATGCCGATATTGTTAGTTTTAAGACATCAGTAGACTGGTTTTTTTGCCA
+CCAGCTTCT
+>F2YP0BU02JDE7P length=88 xy=3726_1203 region=2 run=R_2009_09_24_17_10_49_
+GAATGGAATCATCCGTAATTGAATGGAAAGGAATGGAATGGAATGGAATGGAATGGAATG
+GAATGGAATGGAATGGAATGGAATGCGT
+>F2YP0BU02IZKK3 length=117 xy=3568_2149 region=2 run=R_2009_09_24_17_10_49_
+TTTGTAGGATTTTAAGAATCAACAAAATTTTCTTTAAAATAAATCATTGTGTCCCTGTGT
+GTTGAAGTATGGCTTTGGTCAGTCTGTATTTATGTTTTCTTCGAATTCTTCTTAGAA
+>F2YP0BU02IVEHV length=49 xy=3521_0145 region=2 run=R_2009_09_24_17_10_49_
+CGTTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCTATTCGGTT
+>F2YP0BU02GJJC7 length=469 xy=2565_3129 region=2 run=R_2009_09_24_17_10_49_
+TTTTTCTAAAAGACATCTGAATAAGGAGTTCGTAATAACTTCGTATAGCATACATTATAC
+GAAGTTATACGATATTGTCTCTTTAAAAGCTTTAGTTCCTTTTTAAAAATCACACTTGGG
+TCATTATCAATGCTTTTTGCAAGCATCAGCTCTTTCTGGGTTTTAATTTGATGTAATTCA
+TTAGTGTTTCTGACACACCTTACAGGTTTGCACCACTCTCTGAAACTGCCCTTGATTGAG
+TAACCTCCTTGTTCACTTTTCTGACTTATTCTTCTAAAACCTGAGCTCTCCAGTGATTTT
+GGGAGATTTTACCCCTCATTGGTGACTTGAAGTTTCTTCTTCTTATCTTCTTTGCTAGAA
+TAACTTCTTGTTAAACAATCAGAACTCATTGTGTTTCCTCTCTTCTTCCTGAATCCTATT
+GGCTTTTATACATTTTAGGAGCAGAATTGAACTAAAGAATAAAACATGT
+>F2YP0BU02HLBKR length=61 xy=2996_0585 region=2 run=R_2009_09_24_17_10_49_
+CAATGGATTCAACTCGATTGCAATGGAATGGAATAGAATGGAATGGAATGGAATGGAATG
+G
+>F2YP0BU02IFSP4 length=259 xy=3343_1178 region=2 run=R_2009_09_24_17_10_49_
+TTCTTACACCAGCCACTCACTGGCTAGGAATGATGTCAAGAGACGGTTAGCCATCTCTTG
+GAATGCTTCTCAGCAGCAGTCTTACACTTGGAAAAATAGACTCGTTCCTTTCCCCATGGG
+CAAGAATAGATAACAAAAGAAATAAGCTATCAAAACAAGGGCAAAGTTGTCGTATAACTT
+CGTATAATGTATGCTATACGAAGTTATTACGAGAAGAATGTAGCACAAATTTCTTGAGGA
+AACACAAAGAACTTCATGC
+>F2YP0BU02HV3I0 length=372 xy=3118_3658 region=2 run=R_2009_09_24_17_10_49_
+TTTGTGGAAGTGGACATTTCGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATA
+CGATCATCATCAAAATGTAGAGAGAAGCACTATTAGAAACTACTTGGTGATATCTGCATT
+CAAGTCACAGAGTTGAACATTCCCTTACTTTGAGCACGTTTGAAACACTCTTTTGGAAGA
+ATCTGGAAGTGGACATTTGGAGCGCTTTGATGCCTTTGGTGAAAAGGAAACGTCTTCCAA
+TAAAAGCCAGACAGAAGCATTCTCAGAAACTTGTTCGTGATGTGTGTACTCAACTAAAAG
+AGTTGAACCTTTCTATTGATAGAGCAGTTTTGAAACACTCTTTTTGTGGATTCTGCAAGT
+GGATATTTGGAT
+>F2YP0BU02GJRKA length=308 xy=2568_1464 region=2 run=R_2009_09_24_17_10_49_
+ATTGTGGTCAGAACAATACTCAATATAATTTAAATCTTATATTATTCAAGAATTGTTTGT
+GGCCTAACGTGTGATCTGTCCTAGAGATTGTCTCATGTGCAGTTGAGAAGAATGTACATT
+CTTCAGCTGTTGGATGGAATGTTTTGTATATGTCTGTTAGGTTCATTTGATCTAGAATGT
+AGATTAACTAGGATGTTGATTTATTTCTGTCTAGATGACAGAAAATTCTGGTCGTATAAC
+TTCGTATAATGTATGCTATACGAAGTTATTACGAATGATGCGCTTCAAAGAGTTGTCTTC
+TATGCTTT
+>F2YP0BU02I60SJ length=372 xy=3653_1585 region=2 run=R_2009_09_24_17_10_49_
+TTTTGAAGGAGCAGTTTTGAAACCCTCTTTTCTGGAATCTGCAAGAGTATATTTGCCTAG
+CCTTGAGGATTTCGTTGGAAACGGGATTGTCTTCAGATAAAATCTAGACAGAAGCATTCT
+CAGAAACTTCTTTGGGATGTTTGCATTCAAGTCACAGAGCAGAACATTCCCTTTGGTAGA
+GCAGGTTTGAAACACTCTTTTTTAGTATATGGAAGTGGACATTTGGAGCGCTTTCAGGCC
+TACGTTGGAAAAGGAAACGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAG
+ATTTCGTTGGAAGCGGGAATTCGATACAAATTGCAGACTGCAGCGTTCTGAGAAACATCT
+TTGTGATGTTTG
+>F2YP0BU02FZ6UJ length=56 xy=2345_1561 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTACCTGGTGAACGATGTGACTGTCTCACAGATTTTTAAAATATGTAATGAC
+>F2YP0BU02FYXT9 length=243 xy=2331_0575 region=2 run=R_2009_09_24_17_10_49_
+AGAAGAATTTCTGAGAATGCTGCTGTCTACCTTTATTTGAATTCCCGCTTCCAACGAATC
+CTCCAAGCTATCCAAATATCCACCTGCATTTTCCACAAAAGAGTGTTTCAAAACTGCTCT
+ATCAATAGAAATGTTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATG
+AAAGGGAATCTTCAACTCTATGAGTTGAAGGCAGACATCAGAAAGAAATTTCTGAGAATG
+CTG
+>F2YP0BU02GP5KL length=263 xy=2641_0547 region=2 run=R_2009_09_24_17_10_49_
+AACCAGAATGGATTGGAATATAATGGAGTGTAAGGGAATTGAATAGAATCAATCTGAATG
+TAATGAAAGGGAATGGAACTGAAGGGAATGGAATGGAATGGAATGGAATGGAATGCAATG
+GAATGGAATCAACCCGAGTGCAATCGAATGGAATACGGAATGGAAATGGTCGTAGTAACT
+TCGTATAATGTATGCTATACGAAGTTATTACGAATGGAGTCATCCGGAATGGAACAGAAA
+GGAATGGAATGGAATGAACTGAN
+>F2YP0BU02JGZBK length=296 xy=3766_3390 region=2 run=R_2009_09_24_17_10_49_
+TTTTGATGCCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAGATCATG
+GATATTCTGGAAATAAAGGCTTTCGAGTAGTATCTTGCATTTTTCTCAACAGATTTCAAG
+TGTTGAACCGTTATAGAGGAACAACGCAAAGGACTAAAATAGTCAAGTAAAGTTGTATGG
+ATGAGAAGAAATGCAACGAAGGGAGTTCATCAAAATGTAGTCTTCTAACCCACATTGGTT
+TGCTAGATAGCATTTAAATTTGAGAGCTTGACTTTGAGGTTGAATATTTAATTTCG
+>F2YP0BU02H0L6E length=52 xy=3170_1460 region=2 run=R_2009_09_24_17_10_49_
+ACATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTGGAGAA
+>F2YP0BU02HOYJH length=292 xy=3037_2379 region=2 run=R_2009_09_24_17_10_49_
+TTACTTAACCTCTCTAGGCCAAACTTTCCTCATCTTTAAAGTGGGGTTAATAAAACTCCG
+CTTCTTATTATGAGGTCTAGATGAGAGAATGTTTGTGAAGTGCTTAACATGGTATGTGGA
+AAGACAGTATTCATTATTCATTAAATCATGACCTATTAGATAAAATAGTTTTTTAGAGGG
+GTTATGTGTGCTATGATTGTGGGAGTTTGGTGGAAGGGATTAACGTAATAACTTCGTATA
+GCATACATTATACGGAAGTTTATACGATGCAATTCAAGTGGAAGCTGTCTTC
+>F2YP0BU02GSQKZ length=282 xy=2670_2305 region=2 run=R_2009_09_24_17_10_49_
+AGATGGCCTTACAAGTATTGCTTTCTGCATTTTATTGAAGAGGAAATGAGACTCAAGGTA
+AATGACTGATTCAATGCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAC
+TTGAATTCCTGAGCTCAGTCCTCCACACTGCAAGTATTACAGGTGTGACCCACTCTGCAG
+CCAGTTTAGGTACTCTATCCTATTTTACAGTTGAAGAAACCGACACCTAGAGGGAAGGTA
+ATTTGCCCAGGTCACATGGCTAGTAATTGATGGGACTGGCAT
+>F2YP0BU02HNS0A length=234 xy=3024_1800 region=2 run=R_2009_09_24_17_10_49_
+AGTAGATAGGCAAGTTCTCTAGGAAATATTACTCATACAGCCTAAGAATGTTAATTTGGC
+TCTCCCTCACTGGCAAGGTAACAAGTCCGTAATAACTTCGCATAGCATACATTATACGAA
+GTTATACGAGAAATGTATTACATAGCCAAATACAGTATGTATAAAATATATATTGCAATA
+TTTCATACTTGTTAGTGAAAATATTTTTACAACGTAGTGCCTCCCAAGTGCAGG
+>F2YP0BU02G28U1 length=206 xy=2790_1035 region=2 run=R_2009_09_24_17_10_49_
+TAATATCTTATGAGTCAAGGACAAACCAAAGAGAAGCCAACAGCATTTTGAACTTCGTAT
+AACTTCGTATAATGTATGCTATACGAAGTTATTACGCTGGGCAACCACTAATCTGTTCTA
+CATCTCTATAGTTATGATATTTTATAAATGCTATATAAATGGAATCATGCAGCATGTATC
+CTTCCGACGATGACTTTTTAATCTCA
+>F2YP0BU02HU8CF length=278 xy=3109_0109 region=2 run=R_2009_09_24_17_10_49_
+ATGGAATGGAGTGGAATGGAATGGAATGGAATGGAACAACCCGAATGAAATGGAATGTAA
+TGGAGAGTAAGGGAGTTGAAAGAATCAATCCGAATGGAATGGAATGGAATGGAATGGAAT
+GGAACGGAATGGAATGGAATGGAATGGAATGGAATGGAATGCAATGGAATGGAATCAACC
+CGAGTACAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATCGTATAAACT
+TCGTATAAATGTATGCTATACGAAGTTATTACGAATGG
+>F2YP0BU02G140S length=444 xy=2777_2650 region=2 run=R_2009_09_24_17_10_49_
+TTTTACACCAGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCAAAAG
+CAATATCCAGTACATCATATGTCGCACATAAGTGTCATTTGCTGTTACTGTTTTTATTAT
+TATTATTAAAGATAAGGAGACTAGATAGGCTTTGAAAAATATATGATGAATTTGTTTTCA
+GTCACTTTGAGTGCTAAATAGAAATTCACTTCCTGAGTTTCTAATGATCGCCATTCTAAC
+TTGTGTGAGGTGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGC
+TGAGCATTTTTTATGTGTCTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGCTC
+ATATCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTCTTGTAAATTTGTTTGAGTTC
+ATTGTAGATTCTGGATATTAGCCC
+>F2YP0BU02HZ20Y length=299 xy=3164_1216 region=2 run=R_2009_09_24_17_10_49_
+ACCAGAGGCTCAAGATACCCAAGTAAATACCCAGGATTTCCAGGGAGAAGTAAAGCAAAG
+ACCTGGCAAGTGTTATCACTGCAGCCATAGTTAATTCAAATGTTCATGGATGCAACTTCA
+ACTATAGACATTTGACCACCTGTTATCGTATAACTTCGTATAATGTATGCTATACGAAGT
+TATTACGGTAAAGCACTGAGAGAAGCGACATTGGAGGAGAGAGAAGGAAGAGAGCCAAGA
+AGGATGAAGGCCCTCTGAGGAGTGAGATGCTTGGTGCTATTGGAAGGAGGATGGAGGGC
+>F2YP0BU02J3VA9 length=291 xy=4027_2227 region=2 run=R_2009_09_24_17_10_49_
+TTTGCTTTCCATTTTTGGCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTAC
+GTCCACCATATTAACTGGCCTTATTAATTTCCTAGGGTTGCCATAACAAAGTACTGTGAA
+CTGGGTGGCATAAAACAGTACAAATTATTCTCATGGTTCTGGGGGCTAGAAGTCCAGAAT
+AAAGGTCTGATAGGATCATGTTCTCTGTGAAAGCAGTTAGAGGAGAATCCTTCCTTGTCT
+CTTTTGGGTTTCTTGTGATTGCCAGCGATCTTTGGTGTTCCTGGCTTGCAA
+>F2YP0BU02FW49S length=358 xy=2310_2910 region=2 run=R_2009_09_24_17_10_49_
+TTCCATTCAAGTCCATTCGCTTCCATTCCATTCCATTCCTTTCCATTCCGTGCCATTCCA
+TTCAATTCTATTCCATTCGACTCCATTCCATTCCATTGCCTTCCATCCGATTCCATTCCA
+TTCTATTCCTTTCCATTCCGTTCAATCACATCCCATTCTTTTCCATTATATTCGAGTCCA
+CTCCACTCCAGTACATTCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
+TTGCTTTCCCAGCCCATTGGCTTAATTCAGCCCTTAATGCTCTTCCCCTTTGGAATGCAG
+GTGGTTTAATGAGAATTTAGGTTCTCAAGTCAGATTGCCTGGGTTCACATCTAGCTTT
+>F2YP0BU02GWHIX length=297 xy=2713_1063 region=2 run=R_2009_09_24_17_10_49_
+TCTTTGGATGTTCCAGTAATGTATGTGTTCAATCCATTTGTCGGTCTTCCATAGTTCTCA
+TTTTCTCTGTAATACTTGAGTTTTGCTTTTCAGATGTTTGCTTAGATAATTTTGTATAAC
+GTAATAACTTCGTATAGCATACATTATACGAAGTTATACGACATCTTGCTTCTTAATTTA
+TTTTATTTTTAAATTTTATTTCATCTAGAGTTTACAATACACATCTTTAACTTATCACAG
+CTCTATGTAGAGTATAAAGAATGTACAGCAGGAGAAGTCAGTTTTTCTCTTCTGTCT
+>F2YP0BU02GIT1L length=445 xy=2557_3079 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTGTTTCCTCAGTTTTTCATTCCTCTGTTTCCCCCTTTCTACCTTCTGTGGGGTTA
+TTTGAACACATTTCTTATCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
+GTGTTGGTATTATCTACATCTAAAAACAAAATTGGCATGGAAGTGGGAATAGAAAGAATG
+AGAAAAGAGGAGGCGAGAGGGTGGCTCAACAGTTGAGACAGGTTTTCAAGAGTAAACCTC
+AAAAGGGCTTCTGGCCAGCAGGGTCAGGAGCAAACTTTTCTATAGCCTGAGGCTTTTTAA
+AGGGCCCGGTGGGGAATTGTGCTTTGAAGCAAGATTCTATTAGGGAGGGTTTGGAGAAGT
+GCTGGCTGTTCTGTTAGGGCCATTATGCTCTGTTGAAGCTATGGGCAGGGGTGACATTCG
+GGGGTTCTGGGCCAGGGTGGCCAAA
+>F2YP0BU02IMSS7 length=364 xy=3423_0201 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGAGACGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGTCA
+ACAAGGCGGCCCCCATAGGCTGGAGGCTATGCTCTGGAGAAGAGTGCACCTGTGAATTCT
+TGACAGAGACTGCTCAGCAGCTGCAGGATGGCTGCACCTCCCTGGTAAGGGAGGTCTATA
+TGTATCAACTGTTCTCAACCTTACAAAATATATTATTTTAACCCCAGTCTTCTAATACAG
+TTGCTTGCTGTATGTTTGGTCCTTAGCAAGACCAGCTTTCCAGAGCAGTGCCCAGGGCTG
+GCTCTAATCACATCACCTTCCTTCTTCCTATCACAATTATCCCCTCTGGATCTCATTTGT
+GGAT
+>F2YP0BU02JTR7A length=406 xy=3912_2676 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTTTTTTGAGGCGGAGTTTTCGCTCTTGTTGCCCAGGTGGGAGTGCAATGGT
+GCAATCTCAGCTCGCCACAACCTCCGCCTCCCGAGTTCAAGCGATTCTCCTACCTCAGCC
+TCCCAAATAGCTGGGATTACAGACATGCACCACCATTGCCTGGCTGATTTTGTATTTTTA
+GTAGAGACGGGGTTTCTCCACGTTGGTCAGGCTGGTCTCGAACTCTCGTATAACTTCGTA
+TAATGTATTGCTATACGAAGTTATTACGCCCAAAATTTACTAAATCAGAATATACATTTT
+AACAAGATTTCCCTGAGTGATTTCTATGCACATTAAAGTTTAAGTTGGTACATTTCTTGA
+CTGGGAATATTACTATGTTACTCGATATTGTCTGGCATGCTGTTAG
+>F2YP0BU02JHSQ4 length=341 xy=3776_0574 region=2 run=R_2009_09_24_17_10_49_
+AATCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTAAGATCATGTCACTGCATTCCA
+GCTTGGGCAACAGAGACTCCATCTACAAAAAGTAAACTATATCCTTAGTCAAGTAATCCC
+ATCGTTAGAACTCTCTGGCCATCGTTCAGTCCGTAATAACTTCGTATAGCATACATTATA
+CGAAGTTATACGATAGCATAATTTGTGTATTTCCCTTAAAATATTAATTTTAATATCCTG
+TGCATCAGGCAGTTTCCTCAGCTCTTATTCTTTATCAGGAACCCTTCCCATGTCTTTTGG
+TTATGATGATATCATTGAATCTACTGGAGTCCAGCAGTGGC
+>F2YP0BU02GDLVC length=394 xy=2498_0870 region=2 run=R_2009_09_24_17_10_49_
+GAAGTAGCTGGGATTACAGGACATGAGCGCAACCAAGAGACATTTTTAAAGTACCAAGTT
+CCCAGGTTCCAATTCTAGACCTACTAAAAGGAAAATTATTCACTGGATGCTTTGGAGGTG
+CTAGACAGCCCTTCTAACACACACACCATGTGCTTTGCTTCCCAAGCACAATTCTCTAGC
+AATAAAAAGGGGACTGTCTAGAATACAACTTACCTGACAAATGATACTCTCTGGCTTGTT
+ACACGAACTATCCGTAATAACTTCGTATAGCATACATTATATGAAGTTATACGAGGATCA
+GCTGTTCACACCATCATGGCCAAGAAAGGCCAAAATAGCCATAGGACTTCTAGAATTTGT
+GGAAGATGTTTTCCAATGGCCACTACGGAAATTT
+>F2YP0BU02H1CSQ length=248 xy=3178_3192 region=2 run=R_2009_09_24_17_10_49_
+TTTCTTTCTAAGCTGAGAAGACCTTTATATATCATATATATAACATATAAATATATATAA
+TTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGATTGACCTGCCTCAG
+CCTCTCAAAGTGTTGAGATTACAGGCCTGAGCTTCTGCTCCCAGCCCACATCCCATTCTT
+GAACATTTAGATGTTCTTCTTTTCCTCCTATAAATAACACAAGTACACAGGAATTTATAA
+TGTCCTCT
+>F2YP0BU02GGAIJ length=65 xy=2528_3241 region=2 run=R_2009_09_24_17_10_49_
+TGTGATGATTGCATTCAAGTCACAGAATTGAACATTCCCTTCTACAGAGCAGGTTTGGTA
+AACAA
+>F2YP0BU02JS9DO length=291 xy=3906_2858 region=2 run=R_2009_09_24_17_10_49_
+ACATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGTTCTACTCTGTGAC
+TTGAATGCAAACATCCCAAAGAAGTTTCTGAGAATGCTTCTGTCTAGATTTTCTCTGAAG
+ACAATCCCGTTTCCAACGAAATCCTCAAGGCTAGGCAAATATACTCTTGCAGATTCCAGA
+AAAAGAGTGTTTCAAAACTGCTCCTTCAAAACGGTGGTTCAATTCTCTTAGTTGAGTACA
+CACATCTCAAATTAGTTTCTGAGAATGCTTCTGCCTAGTTGTTACGGGAAG
+>F2YP0BU02GM4B1 length=165 xy=2606_2335 region=2 run=R_2009_09_24_17_10_49_
+TTTTGGAGCTCACAGAGTCCTATACTGAAAACTGAATATCCCACAATAAAACTAGAAAGA
+AGATTCCTGTTAAACTACTATGTGCGTAATAACTTCGTATAGCATACATTATACGAAGTT
+ATACGAGTTTGTGATGTGGGTATTCAGCTCATAAATTAAAACCTT
+>F2YP0BU02HGA3Q length=248 xy=2939_0164 region=2 run=R_2009_09_24_17_10_49_
+AGTTGTCTCTCTTTAAAGAGAGAGATGGCTGGTCACGGGGCTCCTGTCTGTAATCTCAGC
+GCTTCAGGAGGCTGAGCGGAAGGATCGCTTGAGATCAGGAGTTCAATACCATTCTGGGCA
+ACATAGCGAGACCCCTGACTCGACAGAAAAATACCAAACGTAATAACTTCGTATAGCATA
+CATTATACGAAGTTATACGAACTTATATGTGTTCTTTTGAGAAGTATCTGTTCATGTCCT
+TTGCTCAC
+>F2YP0BU02H0Y31 length=236 xy=3174_1839 region=2 run=R_2009_09_24_17_10_49_
+TCTGTGTCTGTTTGTTCTGTGCTGTATCCTAGAATTTAGCACAGTGCCTGGTATGTCAGA
+CATTACTAAATATAGATTGACTGAATGCAATGCCTATTAGATGAACTAGTGAATCGTNTA
+ACTTCGTATAATGTATGCTATACGAAGTTATTACGGAGGAGGTACAGCATTGACAATGTC
+TTTCTGAATTATCCTTATCTTTGGGAGGCAATCCTTATACCCTAGCTGCAGAGATA
+>F2YP0BU02IYXL2 length=83 xy=3561_1048 region=2 run=R_2009_09_24_17_10_49_
+CTTTCAACTAATGGTGCCAAGATAATTGGTAAGCTACATGTAGAATTACGAAACTGGATA
+ATCATCTCTCACCTTATACAAAA
+>F2YP0BU02HJR12 length=382 xy=2978_2360 region=2 run=R_2009_09_24_17_10_49_
+TTTACTTATAATGCCTAATACAATGTAAAGGCTGTGGAATAGTTGTAATACTATTGCATT
+TAAAATTCATTTTATTTTTAATTGTTGTAGCATTATTTTTGTTTCTGTTCTAAAATATTT
+TCAATCCACAGTTGAATACAGAACCTGCAGCTACAGAGGGCTGATTGTACATGAGAAACT
+TCAGAGGAAAATGAAGACACAGAAAGTAGTTGGTTCTAAGTGCTTACACACTAGGTTGAA
+CAAACAGTAGTCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGCAATA
+TGTAAATTACATGCAAGATTTCATTCACCCTTTACCATTTTAGTTCCAGCTGGTATTTGG
+GGTTTTGGAAAAGTCCAAAACT
+>F2YP0BU02F5BIN length=392 xy=2403_3325 region=2 run=R_2009_09_24_17_10_49_
+TTTTCATGGCAGTGCAGTTAATAATCCGTAAGAACAAATATTTTGTTTAAAATTACCTTT
+TGAAATAGCAAAACCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGTT
+AGGTAAGCTGGACTGAGGGACAAGGTCATGTCCTCATAGAAAAGTCACAAACCTCGCTGG
+CTAGTATCTGTGGTTCTGTAGTAGAGGCACTTCTCAGGGTGAAGAGGAGGTGGGTGTTGG
+CCTAGTCCCCAAGCCTTTTTAAATATACATATCAAATTATTAACACCAAAATGAGACATT
+GTTTTTGTTTTAGTTTTGTTTTAATTTTAGAAGTGGGATAGCGGAAAACCCAAAGTGATC
+ATCTGCTCTTAGCACAGAGCTAAGCGTCTAAG
+>F2YP0BU02I8G7G length=386 xy=3669_3978 region=2 run=R_2009_09_24_17_10_49_
+TTTTGCTTAAATACTCTTGGTAATATACTATATACATTATTAGTACACAGAGCAAAACAG
+AAACTGGGGAATCACTTGAGAAACATCATACGTAATAACTTCGTATAGCATACATTATAC
+GAAGTTATACGACGAGAACTACGTGATGCATACACAAGCTTCAATAGCCAATTCGATCAA
+GTGGAAGAAAGGGTATCAGTGATTGTAGATCAAATCAGTGAAATAAAGCGAGAAGGGAAG
+TTTAGAGAAAAAAGAGTAAAAAGAAATCAACAAAGCCTCCAAGAAATATGGGACTATGTA
+AAATGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGACAGGGAGCATGGAACCAAG
+ATGGAAAACACTCTTCAGGATATTAT
+>F2YP0BU02H927V length=466 xy=3278_1081 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTCCTCTTCATTTCTTGGGGGAAGAAGGAACACAGCAAACAGTCACTATAGACAAT
+TATTTAGACATTTCTATTATTATTTAGGGAGAAATTAGGTCGTATAACTTCGTATAATGT
+ATGCTATACGAAGTTATTACGATTGATTTGAAACATTTTTTCTTTTGTAATATACCCATT
+TCATGTTACAGATCTCCCTCTGAGCACTTTTTAGATGATCTCACAAATTTGCATAAATTC
+TGTATTAATTTTTATATAGGTAACATATTTTCTAATTTTTCTTTTGATGTATTTCTTGAC
+ATATCCATGGATTATTTGAAGTATCATGTTTAACTTCTAAATATTTGGGAAATTTTTAGG
+GTATCTTTCTATTATTAATTTCTAATTTCATTCTGTTGTGGATAGACAACATATATTGTA
+TAATTTCAATCATTTTAACTTTACTGAAATTTGTTTTATTGTTACT
+>F2YP0BU02HOCK5 length=284 xy=3030_2599 region=2 run=R_2009_09_24_17_10_49_
+TTCCCATGGAGCACTGCATGGAAGCCCCAGGGGGCCGTACCCATGTCACCGGCACTCCAT
+GTGTGGGTGGAGATCTCCAACTCCAACAAAAGATAGAGCTCTCTTGGCAGGAATGACAAG
+TGACAAAGTTCTCTATCTTACCCCGTGCCTTAAAATGATCATCTGAGTGTCCCAGAGTAA
+ACAGTAGTATTTGTAAAAATAAAAATATATATTTTTCTATTGAATATGTATATATACGTA
+ATAACTTCGTATAGCATACATTATACGAAGTTATACGAATGACG
+>F2YP0BU02G2GAG length=146 xy=2781_0870 region=2 run=R_2009_09_24_17_10_49_
+CAACATGAAATCCTATTTTAAGATCCTAAACTTCAGTTTATAAACTCGTATAACTTCGTA
+TAATGTATGCTATACGAAGTTATTACGATAGGGTGATGTATATATCTATTTCTACCCTAA
+ATAAGGAAAGCTGCAACTTTTTTCTT
+>F2YP0BU02JVSW4 length=224 xy=3935_2710 region=2 run=R_2009_09_24_17_10_49_
+AGCAGGACTCAGAGTCTGGTGGAAAGATAATTTATATAATATTTATAATGTAATAATGAA
+TTAATACTACCTAAATTGAACCATACGTAATAACTTCGTATAGCATACATTATACGAAGT
+TATACGAGGCTCAGGCAGGATTATTTGAACCAGGAGATACCGGTGTCAGGAAAGCAAAAC
+CCAGCATTTTGGGAGGCTCAGGCAGGATTGTTTGAAACCAACTT
+>F2YP0BU02G47T9 length=277 xy=2812_2911 region=2 run=R_2009_09_24_17_10_49_
+AACAATGTGAATAGTTCTGAAATAATGTCGTATAACTTCGTATAATGTATGCTATACGAA
+GTTATTACGGGCTCTGTGGGAGATGCAGTGGAAGCTTCAATTAGCCAAGTGGAAGTTTCT
+ATTACAAATAAATAAGCATTTAGTTAATTTCTTAGCATAATGAATGTGGTTTTAGAGGTT
+TCAGGATATGCACTATTCAATTCTCATTAGCCTTTTTATTGTCATCTTTATTCATCAGTT
+GTGGTGCCACTTGCCATGTAATGTTTTCCTTCTATCC
+>F2YP0BU02GKDRF length=348 xy=2575_1561 region=2 run=R_2009_09_24_17_10_49_
+ATGATCACCACGAGTTACAGATTTCTTTGTTCCCTCTCCATTCCCACTGCTTCACTTGAC
+TAGCCTAATCCTTCCAAAGGAAACGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGATGCCTTAGTTTGATATTGTAAATATCACAATATCACAATTGTCACAACATTTACA
+ATATCAAAATAAGCCAGGAATACCAAAAATTAAACCCACATGTCAATTTGAGAAAAATTT
+ATAGGACTATGACATGCATTAATTTGTCTTCTAAAAAATCTTCCATTAAAGTGTTGTATT
+TTTTCTTTTGATTCCTTCATTACATCAGGCTCTGTCCTTGAATTCCTT
+>F2YP0BU02I6CRD length=70 xy=3645_3207 region=2 run=R_2009_09_24_17_10_49_
+ATTCTGACTATCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGGGCG
+GACTACTACT
+>F2YP0BU02G63QT length=232 xy=2834_0803 region=2 run=R_2009_09_24_17_10_49_
+ATAAACTAGTATGTTTCCGAGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATT
+ACGCTCTAGTTGTCTGCAATAAATAAATTATCTTGCTGCAAAGATGCAAAGCACATTAGA
+AATTCACCAATCATGTTCTATGGGAAAGTAATTTCAAGAGAGACAAAAAGGGAGATGGAT
+GTTAGAGAGGCAATCCAAAAATGTCTGATATACAAGACAATACACCTTCATC
+>F2YP0BU02GLOJ1 length=75 xy=2590_0767 region=2 run=R_2009_09_24_17_10_49_
+TTTCTGTAGTAACTGGAAGTGAACATTAGGACCGTAATAACTTCGTATAGCATACATTAT
+ACGAAGTTATACGAT
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input3.fasta	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,2 @@
+>linker
+TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input4.qual454
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input4.qual454	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,700 @@
+>F2YP0BU02IPIOC length=313 xy=3454_0058 region=2 run=R_2009_09_24_17_10_49_
+14 14 14 16 16 24 24 30 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 32 32 32 32 40 40 40 40 40 40 40 40
+39 39 38 38 38 40 40 40 40 40 40 40 40 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 38 36 20 20 22 22 22 34 20 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 28 28 28 28 39 39 40 39 39
+39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 36 36 24 24 24 24 30 15 15 15 24 27 38 40 40 31 31 31 31 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 30 30 30 33 33 33 38 38 40 40 20 20 27 26 26 39 40 40 31 31 31 31 40 40 40 35 35 35 35 33 31 20 12 12 12 12 12 20 25 37 34 35 31 31 36 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GASSR length=219 xy=2466_0953 region=2 run=R_2009_09_24_17_10_49_
+35 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 27 26 26 27 33 40 40 36 36 36 32 32 30 30 36 31 29 29 31 36 36 36 36 36 36 33 33 34 34 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 32 24 19 19 19 28 25 27 27 23 23 25 28 34 35 32 30 18 18 20 30 35 40 40 40 40 36 40 38 40 40 40 40 39 30 21 21 21 30 35 40 40 40 40 38 36 36
+40 40 40 36 30 26 26 26 26 30 30 36 36 38 36 36 40 40 36 37 35 39 40 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 30 30 30 33 35 34 40
+>F2YP0BU02HLXG3 length=220 xy=3003_0293 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 39 39 39 34 34 19 16 16 36 40 40 36 27 19 19 19 30 30 36 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 35 21 21 21 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 34 40 40 40 40 40 40 24 20 20 19 19 28 33 38 36 36 36 36 36 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 36 36 40 40 40 30 30 20 20 20 33 36 34 34 34 34 36 40 31 33 33 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40
+40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GF6D7 length=134 xy=2527_1997 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 40 40 40 40 39 30 21 21 21 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 39 39
+>F2YP0BU02G6NFT length=92 xy=2829_0151 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 39
+39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GD65M length=129 xy=2504_3880 region=2 run=R_2009_09_24_17_10_49_
+13 13 13 14 14 14 14 14 14 13 13 18 27 27 25 18 18 22 13 14 14 22 15 17 27 24 30 35 32 32 35 35 38 40 40 36 36 28 28 28 33 40 40 37 37 37 37 39 40 39 40 37 37 37 40 39 40 40 39 39
+37 37 38 32 29 28 27 27 27 36 36 36 36 38 36 36 38 40 29 29 29 27 24 19 19 24 33 39 29 29 25 28 33 40 40 40 40 40 38 36 36 36 36 33 35 27 27 14 14 14 14 14 14 11 17 21 24 28 25 26
+27 19 19 22 22 22 29 29 32
+>F2YP0BU02GW28F length=318 xy=2720_0525 region=2 run=R_2009_09_24_17_10_49_
+39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 33 33 40 39 40 21 21 21 21 39 31 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40
+40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 39 39 39 40 40 40 31 31 31 31 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 29 29 29 29 40 40
+40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 40 35 27 33 30 30 31 17 17 19 24 36 32 17 19 19 33 33 38 33 33 34 40 40 40 40 40 40 40 40 40 40 40 40 39 39 26 26 26 26 39 39 40 40 40
+40 38 38 40 40 40 40 40 40 26 26 26 29 29 30 29 29 38 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 36 36 36 30 19 19 19 19 19 36 36 36 38 36 36 36 36 40
+40 40 40 40 40 40 40 40 40 40 40 40 33 33 33 32 40 40
+>F2YP0BU02HKJIX length=388 xy=2987_1095 region=2 run=R_2009_09_24_17_10_49_
+29 29 29 29 39 40 40 40 40 40 40 40 31 31 31 31 39 19 21 21 21 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 34 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 39 39 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40
+40 40 40 40 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 35 30 30 30 39 40 40 40 40 40 40 40 40 40 39 39 39 38 38 38 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 30 30 30 35 40 40 40 40 40 40 39 39 39 40 40 40 39 38 38 39 39 40 40 39 39 39 40 40 39 39 39 40 40 39 39 40 40 40
+40 39 39 39 40 40 40 39 39 37 39 34 39 40 40 36 36 36 36 31 33 26 22 16 16 16 26 22 31 31 32 28 29 24 24 26 36 34 40 40 37 39 39 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40
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+>F2YP0BU02F5BIN length=392 xy=2403_3325 region=2 run=R_2009_09_24_17_10_49_
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+>F2YP0BU02H927V length=466 xy=3278_1081 region=2 run=R_2009_09_24_17_10_49_
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+35 35 35 32 32 32 35 35 35 35 35 35 31 31 31 31 35 32 32 12 12 12 30 32 25 29 20 20 20 25 25 26 30 19 19 13 13 20 9 9 18 13 13 22 24 13
+>F2YP0BU02HOCK5 length=284 xy=3030_2599 region=2 run=R_2009_09_24_17_10_49_
+40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 31 31 28 28 35 22 20 21 20 20 28 28 19 40 35 23 23 23 27 29 33 38 40 40 40 40 28 29 28 30 38 40 40 39 38 38
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+38 37 28 28 29 32 35 40 40 38 40 38 32 33 33 40 38 37 38 37 40 40 40 40 40 40 38 38 38 40 40 40 40 40 40 40 38 38 38 38 40 40 40 38
+>F2YP0BU02G2GAG length=146 xy=2781_0870 region=2 run=R_2009_09_24_17_10_49_
+33 33 35 35 35 32 20 16 15 15 24 27 29 30 29 15 15 15 15 19 19 33 33 32 32 33 33 30 31 31 39 39 37 37 37 37 37 37 37 37 24 21 21 21 31 39 40 40 40 40 39 40 37 37 37 37 37 37 37 37
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+15 27 22 24 19 17 13 13 13 20 22 28 25 25 24 20 20 11 11 11 12 11 11 17 11 11
+>F2YP0BU02JVSW4 length=224 xy=3935_2710 region=2 run=R_2009_09_24_17_10_49_
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+26 33 35 40 40 40 28 31 34 34 39 38 38 39 40 40 40 40 40 39 39 39 40 40 40 39 39 39 39 40 36 34 38 39 38 38 38 39 39 38 38 40 40 40
+>F2YP0BU02G47T9 length=277 xy=2812_2911 region=2 run=R_2009_09_24_17_10_49_
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+34 34 34 34 25 19 20 20 20 17 19 24 20 19 19 20 25 30 23 24 26 31 32 23 23 20 20 20 19 16 14 20 20 25 25 12 12
+>F2YP0BU02GKDRF length=348 xy=2575_1561 region=2 run=R_2009_09_24_17_10_49_
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+17 17 14 14 17 9 9 9 9 20 20 28 28 28 28 25 25 28 36 40 40 40 40 40 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02I6CRD length=70 xy=3645_3207 region=2 run=R_2009_09_24_17_10_49_
+37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 37 37 37
+32 35 25 19 19 19 27 27 18 18
+>F2YP0BU02G63QT length=232 xy=2834_0803 region=2 run=R_2009_09_24_17_10_49_
+35 21 21 20 18 24 27 36 39 38 38 34 29 18 21 21 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 35 34 34 34 38 40 40 40 40
+40 40 40 40 40 40 40 40 40 33 33 32 34 38 36 38 38 36 33 24 17 17 17 27 21 28 28 36 31 24 30 32 34 34 35 35 40 35 33 20 21 21 38 38 40 40 40 36 36 37 40 40 40 38 33 26 26 26 29 36
+35 35 38 38 40 40 37 37 38 37 40 40 40 40 35 32 32 33 37 35 35 19 19 16 28 28 29 24 30 24 24 16 16 16 22 26 28 28 26 32 33 28 28 32 18 18 23 18 18 19 19 19 13 21 34 28 28 28 35 40
+40 40 40 40 40 40 40 40 40 40 38 26 25 25 33 40 25 25 25 25 25 33 33 33 38 40 40 40 40 40 40 40 40 40 38 38 37 40 35 35 33 32 33 31 31 28 28 28 21 25 27 22
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_out1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_out1.sam	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,2 @@
+F2YP0BU02F2LFK	65	chr21	9749451	255	331H34M1I7M	*	0	0	TATCCACTTGCAGATTCCACGAAAACAGTGTTTCAAAAACTG	EEEEEE<787@AAA/../:25////50EGE@CCI::@@@III
+F2YP0BU02GASSR	65	chr21	41805812	255	193H26M	*	0	0	ATCATTGTTGTCTCTCCTGGTGGCAG	IIIIIIIIIIIIIIIIIIH???BDCI
diff -r 765c454bcaa7 -r bb7c2b314e3e tool_conf.xml.sample
--- a/tool_conf.xml.sample	Tue Mar 02 16:35:21 2010 -0500
+++ b/tool_conf.xml.sample	Tue Mar 02 16:40:40 2010 -0500
@@ -203,6 +203,7 @@
   </section>
   <section name="NGS: Mapping" id="solexa_tools">
    <tool file="sr_mapping/lastz_wrapper.xml" />
+   <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
    <tool file="sr_mapping/bowtie_wrapper.xml" />
    <tool file="sr_mapping/bowtie_color_wrapper.xml" />
    <tool file="sr_mapping/bwa_wrapper.xml" />
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_paired_reads_wrapper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,756 @@
+#! /usr/bin/python
+
+"""
+Runs Lastz paired read alignment process
+Written for Lastz v. 1.02.00.
+
+# Author(s): based on various scripts written by Bob Harris (rsharris@bx.psu.edu),
+# then tweaked to this form by Greg Von Kuster (greg@bx.psu.edu)
+
+This tool takes the following input:
+a. A collection of 454 paired end reads ( a fasta file )
+b. A linker sequence ( a very small fasta file )
+c. A reference genome ( nob, 2bit or fasta )
+
+and uses the following process:
+1. Split reads into mates:  the input to this step is the read file XXX.fasta, and the output is three
+   files; XXX.short.fasta, XXX.long.fasta and XXX.mapping.  The mapping file records the information necessary
+   to convert mate coordinates back into the original read, which is needed later in the process.
+
+2. Align short mates to the reference: this runs lastz against every chromosome.  The input is XXX.short.fasta
+   and the reference genome, and the output is a SAM file, XXX.short.sam.
+
+3. Align long mates to the reference: this runs lastz against every chromosome.  The input is XXX.long.fasta
+   and the reference genome, and the output is a SAM file, XXX.long.sam.
+
+4. Combine, and convert mate coordinates back to read coordinates.  The input is XXX.mapping, XXX.short.sam and
+   XXX.long.sam, and the output is XXX.sam.
+
+usage: lastz_paired_reads_wrapper.py [options]
+    --ref_name: The reference name to change all output matches to
+    --ref_source: The reference is cached or from the history
+    --source_select: Use pre-set or cached reference file
+    --input1: The name of the reference file if using history or reference base name if using cached
+    --input2: The reads file to align
+    --input3: The sequencing linker file
+    --input4: The base quality score 454 file
+    --ref_sequences: The number of sequences in the reference file if using one from history 
+    --output: The name of the output file
+    --lastz_seqs_file_dir: Directory of local lastz_seqs.loc file
+"""
+import optparse, os, subprocess, shutil, sys, tempfile, time
+from string import maketrans
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( 'bx-python' )
+from bx.seq.twobit import *
+from bx.seq.fasta import FastaReader
+from galaxy.util.bunch import Bunch
+from galaxy.util import string_as_bool
+
+# Column indexes for SAM required fields
+SAM_QNAME_COLUMN = 0
+SAM_FLAG_COLUMN  = 1
+SAM_RNAME_COLUMN = 2
+SAM_POS_COLUMN   = 3
+SAM_MAPQ_COLUMN  = 4
+SAM_CIGAR_COLUMN = 5
+SAM_MRNM_COLUMN  = 6
+SAM_MPOS_COLUMN  = 7
+SAM_ISIZE_COLUMN = 8
+SAM_SEQ_COLUMN   = 9
+SAM_QUAL_COLUMN  = 10
+SAM_MIN_COLUMNS  = 11
+# SAM bit-encoded flags
+BAM_FPAIRED      =    1    # the read is paired in sequencing, no matter whether it is mapped in a pair
+BAM_FPROPER_PAIR =    2    # the read is mapped in a proper pair
+BAM_FUNMAP       =    4    # the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+BAM_FMUNMAP      =    8    # the mate is unmapped
+BAM_FREVERSE     =   16    # the read is mapped to the reverse strand
+BAM_FMREVERSE    =   32    # the mate is mapped to the reverse strand
+BAM_FREAD1       =   64    # this is read1
+BAM_FREAD2       =  128    # this is read2
+BAM_FSECONDARY   =  256    # not primary alignment
+BAM_FQCFAIL      =  512    # QC failure
+BAM_FDUP         = 1024    # optical or PCR duplicate
+
+# Keep track of all created temporary files so they can be deleted
+global tmp_file_names
+tmp_file_names = []
+
+def stop_err( msg ):
+    sys.stderr.write( "%s" % msg )
+    sys.exit()
+
+def get_tmp_file_name( dir=None, suffix=None ):
+    """
+    Return a unique temporary file name that can be managed.  The
+    file must be manually removed after use.
+    """
+    if dir and suffix:
+        tmp_fd, tmp_name = tempfile.mkstemp( dir=dir, suffix=suffix )
+    elif dir:
+        tmp_fd, tmp_name = tempfile.mkstemp( dir=dir )
+    elif suffix:
+        tmp_fd, tmp_name = tempfile.mkstemp( suffix=suffix )
+    os.close( tmp_fd )
+    tmp_file_names.append( tmp_name )
+    return tmp_name
+
+def run_command( command ):
+    proc = subprocess.Popen( args=command, shell=True, stderr=subprocess.PIPE, )
+    proc.wait()
+    stderr = proc.stderr.read()
+    proc.wait()
+    if stderr:
+        stop_err( stderr )
+
+def split_paired_reads( input2, combined_linker_file_name ):
+    """
+    Given a fasta file of allegedly paired end reads ( input2 ), and a list of intervals
+    showing where the linker is on each read ( combined_linker_file_name ), split the reads into left and right
+    halves.
+    
+    The input intervals look like this.  Note that they may include multiple intervals for the same read
+    ( which should overlap ), and we use the union of them as the linker interval.  Non-overlaps are
+    reported to the user, and those reads are not processed.  Starts are origin zero.
+    
+        #name     strand start len size
+        FG3OYDA05FTEES +   219  42 283
+        FG3OYDA05FVOLL +   263  41 416
+        FG3OYDA05FFL7J +    81  42 421
+        FG3OYDA05FOQWE +    55  42 332
+        FG3OYDA05FV4DW +   297  42 388
+        FG3OYDA05FWAQV +   325  42 419
+        FG3OYDA05FVLGA +    90  42 367
+        FG3OYDA05FWJ71 +    58  42 276
+    
+    The output gives each half-sequence on a separate line, like this.  This allows easy sorting of the
+    sequences by length, after the fact.
+    
+        219 FG3OYDA05FTEES_L TTTAGTTACACTTAACTCACTTCCATCCTCTAAATACGTGATTACCTTTC...
+        22  FG3OYDA05FTEES_R CCTTCCTTAAGTCCTAAAACTG
+    """
+    # Bob says these should be hard-coded.
+    seq_len_lower_threshold = 17
+    short_mate_cutoff = 50
+    # We need to pass the name of this file back to the caller.
+    tmp_mates_file_name = get_tmp_file_name( suffix='mates.txt' )
+    mates_file = file( tmp_mates_file_name, "w+b" )
+    # Read the linker intervals
+    combined_linker_file = file( combined_linker_file_name, "rb" )
+    read_to_linker_dict = {}
+    i = 0
+    for i, line in enumerate( combined_linker_file ):
+        line = line.strip()
+        if line.startswith( "#" ):
+            continue
+        if line.find( '#' ) >= 0:
+            line = line.split( "#", 1 )[0].rstrip()
+        fields = line.split()
+        if len( fields ) != 4:
+            # TODO: Do we want to err out here or just skip the line?
+            stop_err( "Wrong number of fields ( must be 4 ) in line %d: %s" % ( i+1, line ) )
+        name, start, length, size = fields
+        start = int( start )
+        length = int( length )
+        size = int( size )
+        end = start + length
+        if end > size:
+            # TODO: Do we want to err out here or just skip the line?
+            stop_err( "Bad interval in line %d: %s" % ( i+1, line ) )
+        if name not in read_to_linker_dict:
+            read_to_linker_dict[ name ] = ( start, end, size )
+            continue
+        if read_to_linker_dict[ name ] == None:
+            # Read previously marked as non-overlapping intervals, so skip this sequence - see below
+            continue
+        ( s, e, sz ) = read_to_linker_dict[ name ]
+        if sz != size:
+            # This should never occur
+            # TODO: Do we want to err out here or just skip the line?
+            stop_err( "Inconsistent sizes for %s" % name )
+        if s > end or e < start:
+            # Non-overlapping intervals, so skip this sequence
+            read_to_linker_dict[ name ] = None
+            continue
+        read_to_linker_dict[ name ] = ( min( s, start ), max( e, end ), size )
+    combined_linker_file.close()
+    # We need to pass the name of this file back to the caller.
+    tmp_mates_mapping_file_name = get_tmp_file_name( suffix='mates.mapping' )
+    mates_mapping_file = file( tmp_mates_mapping_file_name, 'w+b' )
+    # Process the sequences
+    seqs = 0
+    fasta_reader = FastaReader( file( input2, 'rb' ) )
+    while True:
+        seq = fasta_reader.next()
+        if not seq:
+            break
+        seqs += 1
+        if seq.name not in read_to_linker_dict:
+            if seq.length > seq_len_lower_threshold:
+                mates_file.write( "%-3d %s   %s\n" % ( seq.length, seq.name, seq.text ) )
+            read_to_linker_dict[ seq.name ] = ""
+            continue
+        if read_to_linker_dict[ seq.name ] == "":
+            # TODO: Do we want to err out here or just skip the line?
+            stop_err( "Multiple sequences named %s" % seq.name )
+        if read_to_linker_dict[ seq.name ] == None:
+            # Read previously marked as non-overlapping intervals, so skip this sequence - see above
+            continue
+        ( start, end, size ) = read_to_linker_dict[ seq.name ]
+        if seq.length != size:
+            # TODO: Do we want to err out here or just skip the line?
+            combined_linker_file.close()
+            mates_file.close()
+            mates_mapping_file.close()
+            stop_err( "Sequence disagrees with size for sequence %s, size: %s seq.length: %s" % ( seq.name, str( size ), str( seq.length ) ) )
+        left = seq.text[ :start ]
+        right = seq.text[ end: ]
+        left_is_small = len( left ) <= seq_len_lower_threshold
+        right_is_small = len( right ) <= seq_len_lower_threshold
+        if left_is_small and right_is_small:
+            continue
+        if not left_is_small:
+            mates_file.write( "%-3d %s %s\n" % ( len( left ), seq.name + "_L", left ) )
+            mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_L", seq.name, 0, size - start ) )
+        if not right_is_small:
+            mates_file.write( "%-3d %s %s\n" % ( len( right ), seq.name + "_R", right ) )
+            mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_R", seq.name, end, 0 ) )
+        read_to_linker_dict[ seq.name ] = ""
+    combined_linker_file.close()
+    mates_file.close()
+    mates_mapping_file.close()
+    # Create temporary files for short and long mates
+    tmp_mates_short_file_name = get_tmp_file_name( suffix='mates.short' )
+    tmp_mates_long_file_name = get_tmp_file_name( suffix='mates.long' )
+    tmp_mates_short = open( tmp_mates_short_file_name, 'w+b' )
+    tmp_mates_long = open( tmp_mates_long_file_name, 'w+b' )
+    i = 0
+    for i, line in enumerate( file( tmp_mates_file_name, 'rb' ) ):
+        fields = line.split()
+        seq_len = int( fields[0] )
+        seq_name = fields[1]
+        seq_text = fields[2]
+        if seq_len <= short_mate_cutoff:
+            tmp_mates_short.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
+        else:
+            tmp_mates_long.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
+    tmp_mates_short.close()
+    tmp_mates_long.close()
+    return tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name
+
+def align_mates( input1, ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name ):
+    tmp_align_file_names = []
+    if ref_source == 'history':
+        # Reference is a fasta dataset from the history
+        # Create temporary files to contain the output from lastz executions
+        tmp_short_file_name = get_tmp_file_name( suffix='short_out' )
+        tmp_align_file_names.append( tmp_short_file_name )
+        tmp_long_file_name = get_tmp_file_name( suffix='long_out' )
+        tmp_align_file_names.append( tmp_long_file_name )
+        seqs = 0
+        fasta_reader = FastaReader( open( input1 ) )
+        while True:
+            # Read the next sequence from the reference dataset.  Note that if the reference contains
+            # a small number of chromosomes this loop is ok, but in many cases the genome has a bunch
+            # of small straggler scaffolds and contigs and it is a computational waste to do each one
+            # of these in its own run.  There is an I/O down side to running by subsets (even if they are
+            # one sequence per subset), compared to splitting the reference into sizes of 250 mb.  With
+            # the subset action, lastz still has to read and parse the entire file for every run (this
+            # is true for fasta, but for .2bit files it can access each sequence directly within the file,
+            # so the overhead is minimal).
+            """
+            :> output_file  (this creates the output file, empty)
+            while there are more sequences to align
+                find the next sequences that add up to 250M, put their names in farf.names
+                lastz ${refFile}[subset=farf.names][multi][unmask] ${matesPath}/${matesFile} ... 
+                  >> output_file
+            """
+            seq = fasta_reader.next()
+            if not seq:
+                break
+            seqs += 1
+            # Create a temporary file to contain the current sequence as input to lastz
+            tmp_in_fd, tmp_in_file_name = tempfile.mkstemp( suffix='seq_%d_in' % seqs )
+            tmp_in_file = os.fdopen( tmp_in_fd, 'w+b' )
+            tmp_in_file.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
+            tmp_in_file.close()
+            # Align short mates
+            command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_short_file_name )
+            command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
+            command += '>> %s' % tmp_short_file_name
+            run_command( command )
+            # Align long mates
+            command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_long_file_name )
+            command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
+            command += '>> %s' % tmp_long_file_name
+            run_command( command )
+            # Remove the temporary file that contains the current sequence
+            os.remove( tmp_in_file_name )
+    else:
+        # Reference is a locally cached 2bit file, split lastz calls across number of chroms in 2bit file
+        tbf = TwoBitFile( open( input1, 'rb' ) )
+        for chrom in tbf.keys():
+            # Align short mates
+            tmp_short_file_name = get_tmp_file_name( suffix='short_vs_%s' % chrom )
+            tmp_align_file_names.append( tmp_short_file_name )
+            command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_short_file_name )
+            command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
+            command += '> %s' % tmp_short_file_name
+            run_command( command )
+            # Align long mates
+            tmp_long_file_name = get_tmp_file_name( suffix='long_vs_%s' % chrom )
+            tmp_align_file_names.append( tmp_long_file_name )
+            command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_long_file_name )
+            command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
+            command += '> %s' % tmp_long_file_name
+            run_command( command )
+    return tmp_align_file_names
+
+def paired_mate_unmapper( input2, input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, output ):
+    """
+    Given a SAM file corresponding to alignments of *subsegments* of paired 'reads' to a reference sequence,
+    convert the positions on the subsegments to positions on the reads.  Also (optionally) add quality values.
+    
+    The input file is in SAM format, as shown below.  Each line represents the alignment of a part of a read
+    to a reference sequence.  Read pairs are indicated by suffixes in their names.  Normally, the suffixes _L
+    and _R indicate the left and right mates of reads (this can be overridden with the --left and --right
+    options).  Reads that were not mates have no suffix.
+    
+        (SAM header lines omitted)
+        F2YP0BU02G7LK5_R 16 chr21 15557360 255 40M          * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT           *
+        F2YP0BU02HXV58_L 16 chr21 15952091 255 40M6S        * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat     *
+        F2YP0BU02HREML_R 0  chr21 16386077 255 33M5S        * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc             *
+        F2YP0BU02IOF1F_L 0  chr21 17567321 255 7S28M        * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC                *
+        F2YP0BU02IKX84_R 16 chr21 18491628 255 22M1D18M9S   * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt  *
+        F2YP0BU02GW5VA_L 16 chr21 20255344 255 6S32M        * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA             *
+        F2YP0BU02JIMJ4_R 0  chr21 22383051 255 19M          * 0 0 CCCTTTATCATTTTTTATT                                *
+        F2YP0BU02IXZGF_L 16 chr21 23094798 255 13M1I18M     * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT                   *
+        F2YP0BU02IODR5_L 0  chr21 30935325 255 37M          * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA              *
+        F2YP0BU02IMZBL_L 16 chr21 31603486 255 28M1D1M      * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG                      *
+        F2YP0BU02JA9PR_L 16 chr21 31677159 255 23M          * 0 0 CACACCTGTAACCCCAGCACTTT                            *
+        F2YP0BU02HKC61_R 0  chr21 31678718 255 40M          * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT           *
+        F2YP0BU02HKC61_R 0  chr21 31678718 255 40M          * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT           *
+        F2YP0BU02HVA88   16 chr21 31703558 255 1M1D35M8S    * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat       *
+        F2YP0BU02JDCF1_L 0  chr21 31816600 255 38M          * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT             *
+        F2YP0BU02GZ1GO_R 0  chr21 33360122 255 6S38M        * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC       *
+        F2YP0BU02FX387_L 16 chr22 14786201 255 26M          * 0 0 TGGATGAAGCTGGAAACCATCATTCT                         *
+        F2YP0BU02IF2NE_R 0  chr22 16960842 255 40M10S       * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc *
+        F2YP0BU02F4TVA   0  chr22 19200522 255 49M          * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA  *
+        F2YP0BU02HKC61_R 16 chr22 29516998 255 8S32M        * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG           *
+        F2YP0BU02FS4EM_R 0  chr22 30159364 255 29M          * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG                      *
+        F2YP0BU02G197P_L 0  chr22 32044496 255 40M10S       * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc *
+        F2YP0BU02FIING   16 chr22 45959944 255 3M1I11M1I26M * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG         *
+        F2YP0BU02GUB9L_L 16 chr22 49198404 255 16M1I20M     * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA              *
+    
+    The user must provide a mapping file (which might better be called an unmapping file).  This file is usually
+    created by split_paired_reads, and tells us how to map the subsegments back to original coordinates in a single
+    read (this means the left and right mates were part of a single read).  The mapping file contains four columns.
+    The first two give the mates's name (including the suffix) and the read name.  The last two columns describe how
+    much of the full original sequence is missing from the mate.  For example, in the read below, the left mate is
+    missing 63 on the right (42 for the linker and 21 for the right half).  The right mate is missing 339 on the left.
+    
+        left half:  TTTCAACATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCA
+                    AAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTCGGC
+                    AAAATTCAACAAAACTCCATGCTAAAACTCTCAATAAGGTATTGATGGGA
+                    CATGCCGCATAATAATAAGACATATCTATGACAAACCCACAGCCAATATC
+                    ATGCTGAATGCACAAAAATTGGAAGCATTCCCTTTGAAAACTGGCACAAG
+                    ACTGGGATGCCCTCTCTCACAACTCCTATTCAACATAGTGTTGGAAG
+        linker:     CGTAATAACTTCGTATAGCATACATTATACGAAGTCATACGA
+        right half: CTCCTGCCTCAGCCTCCCGAG
+    
+        mate_name        read_name      offset_to_start offset_from_end
+        F2YP0BU02FS4EM_L F2YP0BU02FS4EM         0              71
+        F2YP0BU02FS4EM_R F2YP0BU02FS4EM       339               0
+    
+    The user can also specify a quality scores file, which should look something like this.  Quality values are presumed
+    to be PHRED scores, written in space-delimited decimal.
+    
+        >F2YP0BU02FS4EM
+        38 38 38 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 38 21 21 21 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 33
+        32 32 40 40 40 21 21 18 18 21 34 34 31 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 32 32 32 32 40 40 40 40 40 40 40 34 34 35
+        31 31 28 28 33 33 33 36 36 36 17 17 17 19 26 36 36 36 40 40 40 40 40 33 34
+        34 34 39 39 39 40 40 40 40 40 33 33 34 34 40 40 40 40 40 40 40 39 39 39 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 39 39 39 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 26 26 26 26 26 40 40 38 38 37 35 33
+        36 40 19 17 17 17 17 19 19 23 30 20 20 20 23 35 40 36 36 36 36 36 36 36 36
+        39 40 34 20 27 27 35 39 40 37 40 40 40 40 40 40 40 40 40 40 34 34 35 39 40
+        40 40 40 40 40 40 39 39 39 40 40 40 40 36 36 32 32 28 28 29 30 36 40 30 26
+        26 26 34 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39
+        40 39 35 34 34 40 40 40 40 30 30 30 35 40 40 40 40 40 39 39 36 40 40 40 40
+        39 39 39 39 30 30 28 35 35 39 40 40 40 40 40 35 35 35
+        >F2YP0BU02G197P
+        40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40
+        40 40 40 40 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 34 40 40
+        40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40
+        40 40 40 40 40 40 40 34 34 34 34 40 40 40 40 34 34 34 34 40 40 40 40 40 40
+        40 40 40 40 40 39 39 39 34 34 34 34 40 40 40 40 39 39 25 25 26 39 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        33 33 33 33 40 35 21 21 21 30 38 40 40 40 40 40 40 40 40 35 35 30 30 30 40
+        40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+        40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40
+        40 40 40 39 39 39 40 40
+        >F2YP0BU02FIING
+        32 32 32 25 25 25 25 24 25 30 31 30 27 27 27 28 28 21 19 19 13 13 13 14 19
+        19 17 19 16 16 25 28 22 21 17 17 18 25 24 25 25 25
+    
+    The output file is also SAM:
+    
+        (SAM header lines omitted)
+        F2YP0BU02G7LK5 81  chr21 15557360 255 40M303H        * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT           D>>>>IIIIIIHHG???IIIIIIIIIHHHFFEIH999HII
+        F2YP0BU02HXV58 145 chr21 15952091 255 226H40M6S      * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat     AA===DDDDAAAAD???:::ABBBBBAAA:888ECF;F>>>?8??@
+        F2YP0BU02HREML 65  chr21 16386077 255 320H33M5S      * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc             HH???HHIIIHFHIIIIIIICDDHHIIIIIIHHHHHHH
+        F2YP0BU02IOF1F 129 chr21 17567321 255 7S28M409H      * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC                4100<<A>4113:<EFGGGFFFHHHHHHDFFFFED
+        F2YP0BU02IKX84 81  chr21 18491628 255 22M1D18M9S341H * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt  ;;;=7@.55------?2?11112GGB=CCCCDIIIIIIIIIHHHHHHII
+        F2YP0BU02GW5VA 145 chr21 20255344 255 286H6S32M      * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA             IIIIIIIHHHIIIIIIICCCCIIIIIIIIIIIIIIIII
+        F2YP0BU02JIMJ4 65  chr21 22383051 255 208H19M        * 0 0 CCCTTTATCATTTTTTATT                                555544E?GE113344I22
+        F2YP0BU02IXZGF 145 chr21 23094798 255 291H13M1I18M   * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT                   IIIIIIIIIIIGG;;;GGHIIIIIGGGIIIII
+        F2YP0BU02IODR5 129 chr21 30935325 255 37M154H        * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA              6...7/--..,30;9<<>@BFFFAAAAHIIIIIH@@@
+        F2YP0BU02IMZBL 145 chr21 31603486 255 342H28M1D1M    * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG                      BB1552222<<>9==8;;?AA=??A???A
+        F2YP0BU02JA9PR 145 chr21 31677159 255 229H23M        * 0 0 CACACCTGTAACCCCAGCACTTT                            IIIIIIIIIIICCCCIIIIIHHH
+        F2YP0BU02HKC61 65  chr21 31678718 255 300H40M        * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT           AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
+        F2YP0BU02HKC61 65  chr21 31678718 255 300H40M        * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT           AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
+        F2YP0BU02HVA88 16  chr21 31703558 255 1M1D35M8S      * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat       >8888DFFHHGFHHHH@@?@?DDC96666HIIIFFFFFFFFFFF
+        F2YP0BU02JDCF1 129 chr21 31816600 255 38M103H        * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT             IIIIIIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIII
+        F2YP0BU02GZ1GO 65  chr21 33360122 255 76H6S38M       * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC       BBBBD?:688CFFFFFFFFFFFFFFFFFFFFFFFFFFDDBBB51
+        F2YP0BU02FX387 145 chr22 14786201 255 201H26M        * 0 0 TGGATGAAGCTGGAAACCATCATTCT                         IIHHHHHHHHHHHHHFFFFFFFFFFF
+        F2YP0BU02IF2NE 65  chr22 16960842 255 209H40M10S     * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc BAAADDDDFDDDDDDBBA889<A?4444000@<>AA?9444;;8>77<7-
+        F2YP0BU02F4TVA 0   chr22 19200522 255 49M            * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA  FFF???FFFFFIIIIIIIIIIIIIIIIIIIIIIIHHIIFHFFFGDDB=5
+        F2YP0BU02HKC61 81  chr22 29516998 255 8S32M300H      * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG           2444<<<<>?>><40009<:8888?A@AAA==:::DB@AA
+        F2YP0BU02FS4EM 65  chr22 30159364 255 339H29M        * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG                      IIIIHHEIIIIHHHH??=DDHIIIIIDDD
+        F2YP0BU02G197P 129 chr22 32044496 255 40M10S258H     * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc IIIIIIIIIIHHHHHHIIIIIIIIIIIII;;;IIIIIIIIIIIIIIIIII
+        F2YP0BU02FIING 16  chr22 45959944 255 3M1I11M1I26M   * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG         :::9:32267=:114244/...446==<<<?@?:9::::AAA
+        F2YP0BU02GUB9L 145 chr22 49198404 255 176H16M1I20M   * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA              IIIIIIIIIHAAC;<</////@4F5778;IIIIIIII
+    
+    """
+    left_suffix       = "_L"
+    right_suffix      = "_R"
+    # Read the mapping
+    mate_to_read_dict = {}
+    i = 0
+    for i, line in enumerate( file( tmp_mates_mapping_file_name, 'rb' ) ):
+        line = line.strip()
+        if not line.startswith( "#" ):
+            fields = line.split()
+            if len( fields ) != 4:
+                stop_err( "Incorrect number of fields (must be 4) in line %s of file %s" % ( i+1, tmp_mates_mapping_file_name ) )
+            mate_name, read_name, s_offset, e_offset = fields
+            if mate_name in mate_to_read_dict:
+                stop_err( "%s is in the mate_to_read_dict when it should not be." % mate_name )
+            mate_to_read_dict[ mate_name ] = ( read_name, int( s_offset ), int( e_offset ) )
+    # Read sequence data
+    read_to_nucs_dict = {}
+    seqs = 0
+    fasta_reader = FastaReader( file( input2, 'rb' ) )
+    while True:
+        seq = fasta_reader.next()
+        if not seq:
+            break
+        seqs += 1
+        seq_text_upper = seq.text.upper()
+        if seq.name in read_to_nucs_dict:
+            if seq_text_upper != read_to_nucs_dict[ seq.name ]:
+                # TODO: Should we err out here or just skip the line?
+                stop_err( "Inconsistent reads named %s (second occurs at line %d in file %s)" % ( seq.name, seqs, input2 ) )
+                #continue
+        read_to_nucs_dict[ seq.name ] = seq_text_upper
+    # Read quality data
+    def quality_sequences( f ):
+        seq_name  = None
+        seq_quals = None
+        line_number = 0
+        for line in f:
+            line_number += 1
+            line = line.strip()
+            if line.startswith( ">" ):
+                if seq_name != None:
+                    yield ( seq_name, seq_quals, seq_line )
+                seq_name  = sequence_name( line )
+                seq_line  = line_number
+                seq_quals = []
+            elif seq_name is None:
+                stop_err( "First quality sequence has no header" )
+            else:
+                seq_quals += [ int( q ) for q in line.split() ]
+        if seq_name is not None:
+            yield ( seq_name, seq_quals, seq_line )
+    def sequence_name( s ):
+        s = s[ 1: ].strip()
+        if not s:
+            return ""
+        else:
+            return s.split()[ 0 ]
+    read_to_quals_dict = {}
+    # TODO: should we use Dan's fastaNamedReader here?
+    for seq_name, quals, line_number in quality_sequences( file( input4 ) ):
+        quals = samify_phred_scores( quals )
+        if seq_name in read_to_quals_dict:
+            if quals != read_to_quals_dict[ seq_name ]:
+                stop_err( "Inconsistent quality sequences named %s (second occurs at line %d in %s)" % ( seq_name, line_number, input4 ) )
+            continue
+        if len( quals ) != len( read_to_nucs_dict[ seq_name ] ):
+            stop_err( "Inconsistent read/quality lengths for %s, quals: %s, read_to_nucs_dict[ seq_name ]: %s" % \
+                      ( seq_name, quals, read_to_nucs_dict[ seq_name ] ) )
+        read_to_quals_dict[ seq_name ] = quals
+    # process the SAM file
+    tmp_align_file_names = ' '.join( tmp_align_file_name_list )
+    combined_chrom_file_name = get_tmp_file_name( suffix='combined_chrom' )
+    command = 'cat %s | grep -v "^@" | sort -k 1 > %s' % ( tmp_align_file_names, combined_chrom_file_name )
+    run_command( command )
+    fout = file( output, 'w+b' )
+    has_non_header = False
+    i = 0
+    for i, line in enumerate( file( combined_chrom_file_name, 'rb' ) ):
+        line = line.strip()
+        if line.startswith( "@" ):
+            if has_non_header:
+                stop_err( "Input SAM contains headers in several places (e.g., line %d) in file %s" % ( i+1, combined_chrom_file_name ) )
+            fout.write( "%s\n" % line )
+            continue
+        has_non_header = True
+        fields = line.split()
+        num_fields = len( fields )
+        if num_fields < SAM_MIN_COLUMNS:
+            stop_err( "Not enough columns at line %d (%d, expected %d)" % ( i+1, num_fields, SAM_MIN_COLUMNS ) )
+        # Set flags for mates
+        try:
+            flag = int( fields[ SAM_FLAG_COLUMN ] )
+        except ValueError:
+            stop_err( "Bad SAM flag at line %d: %s" % ( i+1, line ) )
+        if not( flag & ( BAM_FPAIRED + BAM_FREAD1 + BAM_FREAD2 ) == 0 ):
+            stop_err( "SAM flag indicates reads already paired, at line %d\n%s" % ( i+1, line ) )
+        mate_name = fields[ SAM_QNAME_COLUMN ]
+        unmap_it = False
+        half = None
+        if mate_name.endswith( left_suffix ):
+            flag += BAM_FPAIRED + BAM_FREAD2
+            fields[ SAM_FLAG_COLUMN ] = "%d" % flag
+            unmap_it = True
+            half = "L"
+        elif mate_name.endswith( right_suffix ):
+            flag += BAM_FPAIRED + BAM_FREAD1
+            fields[ SAM_FLAG_COLUMN ] = "%d" % flag
+            unmap_it = True
+            half = "R"
+        on_plus_strand = ( flag & BAM_FREVERSE == 0 )
+        # Convert position from mate to read by adding clipping to cigar
+        if not unmap_it:
+            read_name = mate_name
+        else:
+            try:
+                read_name, s_offset, e_offset = mate_to_read_dict[ mate_name ]
+            except KeyError:
+                stop_err( "'%s' doesn't appear in the mapping file." % mate_name )
+            cigar = fields[ SAM_CIGAR_COLUMN ]
+            cigar_prefix = None
+            cigar_suffix = None
+            if half == "L": 
+                if on_plus_strand:
+                    if s_offset > 0:
+                        cigar_prefix = ( s_offset, "S" )
+                    if e_offset > 0:
+                        cigar_suffix = ( e_offset, "H" )
+                else:
+                    if e_offset > 0:
+                        cigar_prefix = ( e_offset, "H" )
+                    if s_offset > 0:
+                        cigar_suffix = ( s_offset, "S" )
+            elif half == "R": 
+                if on_plus_strand:
+                    if s_offset > 0:
+                        cigar_prefix = ( s_offset, "H" )
+                    if e_offset > 0:
+                        cigar_suffix = ( e_offset, "S" )
+                else:
+                    if e_offset > 0:
+                        cigar_prefix = ( e_offset, "S" )
+                    if s_offset > 0:
+                        cigar_suffix = ( s_offset, "H" )
+            else:               
+                if on_plus_strand:
+                    if s_offset > 0:
+                        cigar_prefix = ( s_offset, "S" )
+                    if e_offset > 0:
+                        cigar_suffix = ( e_offset, "S" )
+                else:
+                    if e_offset > 0:
+                        cigar_prefix = ( e_offset, "S" )
+                    if s_offset > 0:
+                        cigar_suffix = ( s_offset, "S" )
+            if cigar_prefix != None:
+                count, op = cigar_prefix
+                cigar = prefix_cigar( "%d%s" % ( count, op ), cigar )
+                if op == "S":
+                    refPos = int( fields[ SAM_POS_COLUMN ] ) - count
+                    fields[ SAM_POS_COLUMN ] = "%d" % refPos
+            if cigar_suffix != None:
+                count, op = cigar_suffix
+                cigar = suffix_cigar( cigar,"%d%s" % ( count, op) )
+            fields[ SAM_QNAME_COLUMN ] = read_name
+            fields[ SAM_CIGAR_COLUMN ] = cigar
+        # Fetch sequence and quality values, and flip/clip them
+        if read_name not in read_to_nucs_dict:
+            stop_err( "Missing sequence for '%s'" % read_name )
+        nucs = read_to_nucs_dict[ read_name ]
+        if not on_plus_strand:
+            nucs = reverse_complement( nucs )
+        quals = None
+        if read_to_quals_dict != None:
+            if read_name not in read_to_quals_dict:
+                stop_err( "Missing quality values for '%s'" % read_name )
+            quals = read_to_quals_dict[ read_name ]
+            if not on_plus_strand:
+                quals = reverse_string( quals )
+        cigar = split_cigar( fields[ SAM_CIGAR_COLUMN ] )
+        nucs, quals = clip_for_cigar( cigar, nucs, quals )
+        fields[ SAM_SEQ_COLUMN ] = nucs
+        if quals != None:
+            fields[ SAM_QUAL_COLUMN ] = quals
+        # Output the line
+        fout.write( "%s\n" % "\t".join( fields ) )
+    fout.close()
+
+def prefix_cigar( prefix, cigar ):
+    ix = 0
+    while cigar[ ix ].isdigit():
+        ix += 1
+    if cigar[ ix ] != prefix[ -1 ]:
+        return prefix + cigar
+    count = int( prefix[ :-1 ] ) + int( cigar[ :ix ] )
+    return "%d%s%s" % ( count, prefix[ -1 ], cigar[ ix+1: ] )
+
+def suffix_cigar( cigar, suffix ):
+    if cigar[ -1 ] != suffix[ -1 ]:
+        return cigar + suffix
+    ix = len( cigar ) - 2
+    while cigar[ix].isdigit():
+        ix -= 1
+    ix += 1
+    count = int( cigar[ ix:-1 ] ) + int( suffix[ :-1 ] )
+    return "%s%d%s" % ( cigar[ :ix ], count, suffix[ -1 ] )
+
+def split_cigar( text ):
+    fields = []
+    field  = []
+    for ch in text:
+        if ch not in "MIDHS":
+            field += ch
+            continue
+        if field == []:
+            raise ValueError
+        fields += [ ( int( "".join( field ) ), ch ) ]
+        field = []
+    if field != []:
+        raise ValueError
+    return fields
+
+def clip_for_cigar( cigar, nucs, quals ):
+    # Hard clip prefix
+    count, op = cigar[0]
+    if op == "H":
+        nucs = nucs[ count: ]
+        if quals != None:
+            quals = quals[ count: ]
+        count, op = cigar[ 1 ]
+    # Soft clip prefix
+    if op == "S":
+        nucs = nucs[ :count ].lower() + nucs[ count: ]
+    # Hard clip suffix
+    count,op = cigar[ -1 ]
+    if op == "H":
+        nucs = nucs[ :-count ]
+        if quals != None:
+            quals = quals[ :-count ]
+        count, op = cigar[ -2 ]
+    # Soft clip suffix
+    if op == "S":
+        nucs = nucs[ :-count ] + nucs[ -count: ].lower()
+    return nucs, quals
+
+def samify_phred_scores( quals ):
+    """
+    Convert a decimal list of phred base-quality scores to a sam quality string.
+    Note that if a quality is outside the dynamic range of sam's ability to
+    represent it, we clip the value to the max allowed.  SAM quality scores
+    range from chr(33) to chr(126).
+    """
+    if min( quals ) >= 0 and max( quals ) <= 126-33:
+        return "".join( [ chr( 33 + q ) for q in quals ] )
+    else:
+        return "".join( [ chr( max( 33, min( 126, 33+q ) ) ) for q in quals ] )
+
+def reverse_complement( nucs ):
+    complementMap = maketrans( "ACGTacgt", "TGCAtgca" )
+    return nucs[ ::-1 ].translate( complementMap )
+
+def reverse_string( s ):
+    return s[ ::-1 ]
+
+def __main__():
+    # Parse command line
+    # input1: a reference genome ( 2bit or fasta )
+    # input2: a collection of 454 paired end reads ( a fasta file )
+    # input3: a linker sequence ( a very small fasta file )
+    # input4: a base quality score 454 file ( qual454 )
+    parser = optparse.OptionParser()
+    parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
+    parser.add_option( '', '--ref_source', dest='ref_source', help='The reference is cached or from the history' )
+    parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
+    parser.add_option( '', '--source_select', dest='source_select', help='Use pre-set or cached reference file' )
+    parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
+    parser.add_option( '', '--input2', dest='input2', help='The 454 reads file to align' )
+    parser.add_option( '', '--input3', dest='input3', help='The sequencing linker file' )
+    parser.add_option( '', '--input4', dest='input4', help='The base quality score 454 file' )
+    parser.add_option( '', '--output', dest='output', help='The output file' )
+    parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' )
+
+    ( options, args ) = parser.parse_args()
+    if options.ref_name != 'None':
+        ref_name = '[nickname=%s]' % options.ref_name
+    else:
+        ref_name = ''
+    if options.ref_source == 'history':
+        # Reference is a fasta dataset from the history
+        try:
+            # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
+            error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
+            ref_sequences = int( options.ref_sequences )
+            if ref_sequences < 1:
+                stop_err( error_msg )
+        except:
+            stop_err( error_msg )
+    else:
+        ref_sequences = 0
+    tmp_w12_name = get_tmp_file_name( suffix='vs_linker.W12' )
+    tmp_T1_name = get_tmp_file_name( suffix='vs_linker.T1' )
+    # Run lastz twice ( with different options ) on the linker sequence and paired end reads,
+    # looking for the linker ( each run finds some the other doesn't )
+    command = 'lastz %s %s W=12 --notrans --exact=18 --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
+        ( options.input3, options.input2, tmp_w12_name )
+    run_command( command )
+    command = 'lastz %s %s T=1 --match=1,2 O=1 E=2 X=15 K=10 Y=15 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
+        ( options.input3, options.input2, tmp_T1_name )
+    run_command( command )
+    # Combine the alignment output from the two lastz runs
+    tmp_combined_linker_file_name = get_tmp_file_name( suffix='vs_linker' )
+    command = 'cat %s %s | sort -u > %s' % ( tmp_w12_name, tmp_T1_name, tmp_combined_linker_file_name )
+    run_command( command )
+    # Use the alignment info to split reads into left and right mates
+    tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name = split_paired_reads( options.input2, tmp_combined_linker_file_name )
+    # Align mates to the reference - tmp_align_file_names is a list of file names created by align_mates()
+    tmp_align_file_name_list = align_mates( options.input1, options.ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name )
+    # Combine and convert mate coordinates back to read coordinates
+    paired_mate_unmapper( options.input2, options.input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, options.output )
+    # Delete all temporary files
+    for file_name in tmp_file_names:
+        os.remove( file_name )
+
+if __name__=="__main__": __main__()
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_paired_reads_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml	Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,371 @@
+<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0">
+    <description> map short paired reads against reference sequence</description>
+    <command interpreter="python">lastz_paired_reads_wrapper.py
+#if $seq_name.how_to_name=="yes":
+--ref_name=$seq_name.ref_name 
+#else:
+--ref_name="None" 
+#end if
+--ref_source=$source.ref_source --input2=$input2 --input3=$input3 --input4=$input4
+#if $source.ref_source=="history":
+--input1=$source.input1
+--ref_sequences=$input1.metadata.sequences 
+#else:
+--input1=$source.input1_2bit
+--ref_sequences="None" 
+#end if
+--output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}
+    </command>
+    <inputs>
+        <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
+        <conditional name="source">
+            <param name="ref_source" type="select" label="Against reference sequences that are">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+            </param>
+            <when value="cached">
+                <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_file="lastz_seqs.loc">
+                        <column name="value" index="1" />
+                        <column name="name" index="0" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
+            </when>
+        </conditional>
+        <param name="input3" format="fasta" type="data" label="Linker file" />
+        <param name="input4" format="qual454" type="data" label="Select a base quality score 454 dataset" />
+        <conditional name="seq_name">
+            <param name="how_to_name" type="select" label="Do you want to modify reference name?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="sam" name="output1" />
+    </outputs>
+    <requirements>
+        <requirement type="binary">lastz</requirement>
+    </requirements>
+    <tests>
+        <test>
+            <!--
+                input1: a reference genome ( 2bit or fasta )
+                input2: a collection of 454 paired end reads ( a fasta file )
+                input3: a linker sequence ( a very small fasta file )
+                input4: a base quality score 454 file ( qual454 )
+            -->
+            <param name="input2" value="lastz_paired_input2.fasta" ftype="fasta" />
+            <param name="ref_source" value="cached" />
+            <param name="input1_2bit" value="hg18Chr21" />
+            <param name="input3" value="lastz_paired_input3.fasta" ftype="fasta" />
+            <param name="input4" value="lastz_paired_input4.qual454" ftype="qual454" />
+            <param name="how_to_name" value="no" />
+            <output name="output1" file="lastz_paired_out1.sam" />
+        </test>
+    </tests>
+    <help>
+        
+**What it does**    
+        
+**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive `documentation`__ on LASTZ available, although it hasn't been updated for the version of LASTZ that Galaxy is running (the key changes have to do with output formats, so it is still extremely helpful).
+
+ .. __: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01...
+ 
+------
+
+**Input formats**
+
+LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
+
+------
+
+**Outputs**
+
+LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
+
+**SAM output**
+
+SAM has 12 columns::
+
+                                   1     2     3         4   5    6  7         8     9                                    10                                     11  12
+  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  HWI-EAS91_1_30788AAXX:1:2:1670:915    99  chr9  58119878  60  36M  =  58120234   392  GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT   IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII  XT:A:U  NM:i:0  SM:i:37  AM:i:37  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:36
+  HWI-EAS91_1_30788AAXX:1:2:1670:915   147  chr9  58120234  60  36M  =  58119878  -392  ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA   IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII  XT:A:U  NM:i:0  SM:i:37  AM:i:37  X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:36
+
+
+where::
+
+     Column  Description
+  ---------  ---------------------------------------------------------------------   
+   1. QNAME  Query (pair) NAME
+   2. FLAG   bitwise FLAG
+   3. RNAME  Reference sequence NAME
+   4. POS    1-based leftmost POSition/coordinate of clipped sequence
+   5. MAPQ   MAPping Quality (Phred-scaled)
+   6. CIGAR  extended CIGAR string
+   7. MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
+   8. MPOS   1-based Mate POSition
+   9. ISIZE  Inferred insert SIZE
+  10. SEQ    query SEQuence on the same strand as the reference
+  11. QUAL   query QUALity (ASCII-33 gives the Phred base quality)
+  12. OPT    variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
+  
+The flags are as follows::
+
+    Flag  Description
+  ------  -------------------------------------
+  0x0001  the read is paired in sequencing
+  0x0002  the read is mapped in a proper pair
+  0x0004  the query sequence itself is unmapped
+  0x0008  the mate is unmapped
+  0x0010  strand of the query (1 for reverse)
+  0x0020  strand of the mate
+  0x0040  the read is the first read in a pair
+  0x0080  the read is the second read in a pair
+  0x0100  the alignment is not primary
+
+**Polymorphism (SNP or differences) output**
+
+Polymorphism output contains 14 columns::
+
+     1     2     3  4     5                                   6   7   8  9  10  11 12                                   13                                    14
+  --------------------------------------------------------------------------------------------------------------------------------------------------------------
+  chrM  2490  2491  +  5386  HWI-EAS91_1_306UPAAXX:6:1:486:822   10  11  -  36  C  A  ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC  ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
+  chrM  2173  2174  +  5386  HWI-EAS91_1_306UPAAXX:6:1:259:1389  26  27  +  36  G  T  GCGTACTTATTCGCCACCATGATTATGACCAGTGTT  GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+
+where::
+
+  1. (chrM)   - Reference sequence id
+  2. (2490)   - Start position of the difference in the reference
+  3. (2491)   - End position of the difference in the reference
+  4. (+)      - Strand of the reference (always plus)
+  5. (5386)   - Length of the reference sequence
+  6. (HWI...) - read id
+  7. (10)     - Start position of the difference in the read
+  8. (11)     - End position of the difference in the read
+  9. (+)      - Strand of the read
+ 10. (36)     - Length of the read
+ 11. (C)      - Nucleotide in the reference
+ 12. (A)      - Nucleotide in the read
+ 13. (ACC...) - Reference side os the alignment
+ 14. (ACC...) - Read side of the alignment
+ 
+**Tabular output**
+
+Tabular output is a tab-separated format with 30 columns::
+
+   1        2  3     4     5     6     7   8                 9              10  11   12   13   14   15   16   17   18  19                20                21   22     23      24      25    26    27    28    29  30
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  14  PHIX174  +  5386  4648  4647  4661  14  ATTTTCGTGATATT    EYKX4VC01BV8HS  +   204  154  153  167  154  153  167  14  ATTTTCGTGATATT    ..............    14M  14/14  100.0%  14/204  6.9%  0/14  0.0%  4494  NA
+  16  PHIX174  +  5386  3363  3362  3378  16  GACGCCGGATTTGAGA  EYKX4VC01AWJ88  -   259   36   35   51  209  208  224  16  GACGCCGGATTTGAGA  ................  16M  16/16  100.0%  16/259  6.2%  0/16  0.0%  3327  NA
+
+The following columns are present::
+
+             Field  Meaning
+  ----------------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+   1.        score  Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
+   2.        name1  Name of the target sequence.
+   3.      strand1  Target sequence strand, either "+" or "−".
+   4.        size1  Size of the entire target sequence.
+   5.       start1  Starting position of the alignment block in the target, origin-one.
+   6.      zstart1  Starting position of the alignment block in the target, origin-zero.
+   7.         end1  Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+   8.      length1  Length of the alignment block in the target (excluding gaps).
+   9.        text1  Aligned characters in the target, including gap characters.
+  10.        name2  Name of the query sequence.
+  11.      strand2  Query sequence strand, either "+" or "−".
+  12.        size2  Size of the entire query sequence.
+  13.       start2  Starting position of the alignment block in the query, origin-one.
+  14.      zstart2  Starting position of the alignment block in the query, origin-zero.
+  15.         end2  Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+  16.      start2+  Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
+  17.     zstart2+  Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
+  18.        end2+  Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
+  19.      length2  Length of the alignment block in the query (excluding gaps).
+  20.        text2  Aligned characters in the query, including gap characters.
+  21.         diff  Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
+  22.        cigar  A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
+  23./24. identity  Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
+  25./26. coverage  Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
+  27./28.  gaprate  Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
+  29.     diagonal  The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
+  30.      shingle  A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.  
+
+-------
+
+**LASTZ Settings**
+
+There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.
+
+**Commonly used settings**
+
+There are seven modes::
+
+  Illumina-Solexa/AB-SOLiD 95% identity
+  Illumina-Solexa/AB-SOLiD 85% identity
+  Roche-454 98% identity
+  Roche-454 95% identity
+  Roche-454 90% identity
+  Roche-454 85% identity
+  Roche-454 75% identity
+
+when deciding which one to use consider the following: a 36 bp read with two difference will be 34/36 = 94% identical to the reference.  
+
+**Full Parameter List**
+
+This modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu.
+
+------
+
+**Do you want to modify reference name?**
+
+This option allows you set the name of the reference sequence manually. This is helpful when, for example, you would like to make reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at UCSC Genome Browser.
+
+------
+
+**LASTZ parameter list**
+
+This is an exhaustive list of LASTZ options. Once again, please note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu::
+
+  target[[s..e]][-]       spec/file containing target sequence (fasta or nib)
+                          [s..e] defines a subrange of the file
+                          - indicates reverse-complement
+                          (use --help=files for more details)
+  query[[s..e]][-]        spec/file containing query sequences (fasta or nib)
+                          if absent, queries come from stdin (unless they
+                          aren't needed, as for --self or --tableonly)
+                          (use --help=files for more details)
+  --self                  the target sequence is also the query
+  --quantum               the query sequence contains quantum DNA
+  --seed=match<length>    use a word with no gaps instead of a seed pattern
+  --seed=half<length>     use space-free half-weight word instead of seed pattern
+  --match=<reward>[,<penalty>]   set the score values for a match (+<reward>)
+                          and mismatch (-<penalty>)
+  --[no]trans[ition][=2]         allow one or two transitions in a seed hit
+                          (by default a transition is allowed)
+  --word=<bits>           set max bits for word hash;  use this to trade time for
+                          memory, eliminating thrashing for heavy seeds
+                          (default is 28 bits)
+  --[no]filter=[<T>:]<M>     filter half-weight seed hits, requiring at least M
+                          matches and allowing no more than T transversions
+                          (default is no filtering)
+  --notwins               require just one seed hit
+  --twins=[<min>:]<maxgap>   require two nearby seed hits on the same diagonal
+                          (default is twins aren't required)
+  --notwins               allow single, isolated seeds
+  --[no]recoverseeds      avoid losing seeds in hash collisions. Cannot be used with --twins
+  --seedqueue=<entries>   set number of entries in seed hit queue
+                          (default is 262144)
+  --anchors=<file>        read anchors from a file, instead of discovering anchors
+                          via seeding
+  --recoverhits           recover hash-collision seed hits
+                          (default is not to recover seed hits)
+  --step=<length>         set step length (default is 1)
+  --maxwordcount=<limit>  words occurring more often than <limit> in the target
+                          are not eligible for seeds
+  --strand=both           search both strands
+  --strand=plus           search + strand only (matching strand of query spec)
+  --strand=minus          search - strand only (opposite strand of query spec)
+                          (by default both strands are searched)
+  --ambiguousn            treat N as an ambiguous nucleotide
+                          (by default N is treated as a sequence splicing character)
+  --[no]gfextend          perform gap-free extension of seed hits to HSPs
+                          (by default no extension is performed)
+  --[no]chain             perform chaining
+  --chain=<diag,anti>     perform chaining with given penalties for diagonal and
+                          anti-diagonal
+                          (by default no chaining is performed)
+  --[no]gapped            perform gapped alignment (instead of gap-free)
+                          (by default gapped alignment is performed)
+  --score[s]=<file>         read substitution scores from a file
+                          (default is HOXD70)
+  --unitscore[s]          scores are +1/-1 for match/mismatch
+  --gap=<[open,]extend>   set gap open and extend penalties (default is 400,30)
+  --xdrop=<score>         set x-drop threshold (default is 10*sub[A][A])
+  --ydrop=<score>         set y-drop threshold (default is open+300extend)
+  --infer[=<control>]     infer scores from the sequences, then use them
+  --inferonly[=<control>]   infer scores, but don't use them (requires --infscores)
+                          all inference options are read from the control file
+  --infscores[=<file>]    write inferred scores to a file
+  --hspthresh=<score>     set threshold for high scoring pairs (default is 3000)
+                          ungapped extensions scoring lower are discarded
+                          <score> can also be a percentage or base count
+  --entropy               adjust for entropy when qualifying HSPs in the x-drop extension 
+                          method
+  --noentropy             don't adjust for entropy when qualifying HSPs
+  --exact=<length>        set threshold for exact matches
+                          if specified, exact matches are found rather than high
+                          scoring pairs (replaces --hspthresh)
+  --inner=<score>         set threshold for HSPs during interpolation
+                          (default is no interpolation)
+  --gappedthresh=<score>  set threshold for gapped alignments
+                          gapped extensions scoring lower are discarded
+                          <score> can also be a percentage or base count
+                          (default is to use same value as --hspthresh)
+  --ball=<score>          set minimum score required of words 'in' a quantum ball
+  --[no]entropy           involve entropy in filtering high scoring pairs
+                          (default is "entropy")
+  --[no]mirror            report/use mirror image of all gap-free alignments
+                          (default is "mirror" for self-alignments only)
+  --traceback=<bytes>     space for trace-back information
+                          (default is 80.0M)
+  --masking=<count>       mask any position in target hit this many times
+                          zero indicates no masking
+                          (default is no masking)
+  --targetcapsule=<capsule_file>   the target seed word position table and seed
+                          (as well as the target sequence)are read from specified file
+  --segments=<segment_file>   read segments from a file, instead of discovering
+                          them via seeding. Replaces other seeding or gap-free extension
+                          options
+  --[no]census[=<file>]     count/report how many times each target base aligns
+                          (default is to not report census)
+  --identity=<min>[..<max>]   filter alignments by percent identity
+                          0<=min<=max<=100;  blocks (or HSPs) outside min..max
+                          are discarded
+                          (default is no identity filtering)
+  --coverage=<min>[..<max>]   filter alignments by percentage pf query covered
+                          0<=min<=max<=100;  blocks (or HSPs) outside min..max
+                          are discarded
+                          (default is no query coverage filtering)
+  --notrivial             do not output trivial self-alignment block if the target and query 
+                          sequences are identical. Using --self enables this option automatically
+  --output=<output_file>  write the alignments to the specified file name instead of stdout
+  --code=<file>           give quantum code for query sequence (only for display)
+  --format=<type>         specify output format; one of lav, axt, maf, maf+, maf-, text,
+                          lav+text, cigar, text, rdplot, general, or general:<fields>
+                          (by default output is LAV)
+  --rdotplot=<file>       create an additional output file suitable for plotting the alignments 
+                          with the R statistical package.
+  --markend               Just before normal completion, write "# lastz end-of-file" to output file
+  --census[=<output_file>]    count and report how many times each target base aligns, up 
+                          to 255. Ns are included in the count
+  --census16[=<output_file>]  count and report how many times each target base aligns, up
+                          up 65 thousand
+  --census32[=<output_file>]  count and report how many times each target bas aligns, up
+                          to 4 billion
+  --writecapsule=<capsule_file>    just write out a targegt capsule file and quit; don't 
+                          search for seeds or perform subsequent stages
+  --verbosity=<level>     set info level (0 is minimum, 10 is everything)
+                          (default is 0)
+  --[no]runtime           report runtime in the output file
+                          (default is to not report runtime)
+  --tableonly[=count]     just produce the target position table, don't
+                          search for seeds
+  --[no]stats[=<file>]    show search statistics (or don't)
+                          (not available in this build)
+  --version               report the program version and quit
+  --help                  list all options
+  --help=files            list information about file specifiers
+  --help=short[cuts]      list blastz-compatible shortcuts
+  --help=yasra            list yasra-specific shortcuts
+
+    </help>
+</tool>
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml	Tue Mar 02 16:35:21 2010 -0500
+++ b/tools/sr_mapping/lastz_wrapper.xml	Tue Mar 02 16:40:40 2010 -0500
@@ -24,8 +24,8 @@
     <inputs>
         <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
         <conditional name="source">
-            <param name="ref_source" type="select" label="Against reference sequences">
-                <option value="cached">that are locally cached</option>
+            <param name="ref_source" type="select" label="Against reference sequences that are">
+                <option value="cached">locally cached</option>
                 <option value="history">in your history</option>
             </param>
             <when value="cached">

    

Greg Von Kuster

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