updated order_pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1856 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/out/order_pairs.out.1 b/bp_test/out/order_pairs.out.1
index e25e55d02e1d10db14690bde01e2b33669599089..49abf3de3c1dfa28f15b3dff1568054d4a7811c0 100644 (file)
--- a/bp_test/out/order_pairs.out.1
+++ b/bp_test/out/order_pairs.out.1
@@ -2,129 +2,167 @@ SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB
 SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+ORDER: paired
 ---
 SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2
+ORDER: paired
 ---
 SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB
 SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+ORDER: paired
 ---
 SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+ORDER: paired
 ---
 SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y
 SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1
+ORDER: paired
 ---
 SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
 SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC
 SEQ_LEN: 50
 SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 1:N:0:TAGCTG
 SEQ: AAACGGATAGGCTTGTTCTTCCAGCAACAACTCGTATTGCTCCAATGCCAGGGCATCAAGCCCGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
 SEQ_LEN: 98
 SCORES: _bbaceceggeccgeZddghaegffiiWdghfff``ffgfacfcffhiihhfi\_e\egfcggde]acdccc^aa_`[`aca_a^b_`bbbbbbbS_b
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 2:N:0:TAGCTG
 SEQ: CCGGGCTTGATGCCCTGGCATTGGAGCAATACGAGTTGTTGCTGGAAGAACAAGCCTATCCGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
 SEQ_LEN: 98
 SCORES: ^^_eee^ccgeggiidfdd_ggfhhhfhifhhfgfggffgdeghe_ebfgedfXZcffdggdT`^aeeee^`bcacc\^Z^a[]Q[`b^]^aaBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 1:N:0:TAGCTG
 SEQ: CGCCTTTTCATCAGCAACAGACAGTTACGACGCATATCGCCACCCAAATGTTTGCCGAGGCTAAACGGGTATTGAAACGCGGTGGCCGCTTGCGTATT
 SEQ_LEN: 98
 SCORES: ___eeeeegagffgghdefb_e_eggia`\egfdhhdf`gdfghihiiib_`gghf``cbcabcbc^^_KW`c]Y_bbcc[a[[_^aa]cccc]__ab
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 2:N:0:TAGCTG
 SEQ: GGCCAAATAACCGCTGCAGTTGCTGCTGATAATTCAGGTGACGGTTAGCCACAATACGCAAGCGGCCACCGCGTTTCAATACCCGTTTAGCCTCGGCA
 SEQ_LEN: 98
 SCORES: bbbeeeeegfgggiehihhef_gfgfhfghdffhihhfXc^egc_cgabgffghhfhfhfg`d^cba_ac^\_W]abcb_bccc]X`bQ]`b`^_a__
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 1:N:0:TAGCTG
 SEQ: CTGGGTGCCACTGTCGCCACCCTGTTAAGTCGTGAACCCGTTACCATCAGCACTGATGCCAACGTCTGGCAGGCCGCCCAGCTAATGACCGAGCAAAA
 SEQ_LEN: 98
 SCORES: _[_cccceeegggffhiiihdfdefhhafeff_efdfgfhifhghhfbgbgdggfdhihhegggeeeebdZ^aaa^_aaX``b]b_bcccXXaV_ccb
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 2:N:0:TAGCTG
 SEQ: AGCCTGGCCCGGATATCCTTGTCAGTGATAATGCCNGTCAGATGCTGCTTGGCATCTAAAATAAGCAAGGATGANACCTTNTGNTCNGTCNNTANCTG
 SEQ_LEN: 98
 SCORES: b__eeeeeggggcgghiiiihefggcgeffagdbfBOY^cffhfgbgfhdggXegghagghfffeggggeXV^_BKZ\_cBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 1:N:0:TAGCTG
 SEQ: TACCTAAAATAATTAATATCTACAATAGAATAAAATCAGGAAATGTTTATGACACCAGCTCGCCTGTCCATGTTCAGCATGGCTCTGCTTGGTGCTTT
 SEQ_LEN: 98
 SCORES: __acceeegcgggiihihifiiiiiiiiiiefihhhhchhdhiafcghidffghhiihidfggighedhdhibdggegdgeeeedddcddccbcccab
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 2:N:0:TAGCTG
 SEQ: CTACCTGTGCAAAAAGCACCAAGCAGAGCCATGCTNAACATGGACAGGCGAGCTGGTGTCATAAACATTTCCTGNTTTTANTCTATNGTAGNTANTAA
 SEQ_LEN: 98
 SCORES: bbbeeeecggfeghfggfhihhieh]ffbeghiiiBOYcfghighfghghaedfeeV^abcccce`bdbdc```BKZ^aaBKW^^aBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 1:N:0:TAGCTG
 SEQ: GGGTTCAGGCGCCCGGACCATTCATAACATTCTGCAAAACAGTTTGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTGATCTCGTATG
 SEQ_LEN: 98
 SCORES: ___J`cccgZccggghhhhffhbghhfeegffdghhfchhhfaffgbb]e`_c\a_\degdddbbb``^aY]bbb_bbbbbbb`bbbb_]`R]^[WR[
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 2:N:0:TAGCTG
 SEQ: AACAAACTGTTTTGCAGAATGTTATGAATGGTCCGNGCGCNTNAACCCAGATCGGAAGAGCGTCGTGTAGGGAANGANGGNNGNNCNCGGNNNNNGNC
 SEQ_LEN: 98
 SCORES: a__eeecegcgegihhifhhfcgdghfffiibgheBPPYcBOBOXaffffgfhhhffa`bfe\^cR]Z]`baZ`BBBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 1:N:0:TAGCTG
 SEQ: GTGCCAAAGAGGTACTGATGCTTTGTTGTTGTGGTTTAGCCGCACATTCAGCCTCGCTGACGGCAGCTAACTGCACATCTTTGGGGATATCCACCAGA
 SEQ_LEN: 98
 SCORES: ^PWYP`R^cRcccgdghS`d_ebc[`ebffddb[ffffagf[O^_Uc`SabeffeegffW\\[XXR^bTGT__]b]_Y_]Zbbba][abb_cbba_aa
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 2:N:0:TAGCTG
 SEQ: GGTGGATATCCCCAAAGATGTGCAGTTAGCTGCCGNCAGCGAGGCTGAATGTGCGGCTAAACCACAACAACAAANCATCANTACCTNTTTGNCANAGA
 SEQ_LEN: 98
 SCORES: ___cc\c`eggcghad`acabgfdg`g^daagaefBPYOafY_fYaa]e\aMWW__[W^Z_RZ^`aa__`Q[`^BBBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 1:N:0:TAGCTG
 SEQ: CCACCTGCCCGGTTTTAAGATGACTGACCGCCGAACCCACAGCTGCAATATGCCCCACCACTTCATGACCAGCCACCAGCGGATACGCCGACATACCC
 SEQ_LEN: 98
 SCORES: _Z_cccccaY_^cghhbagg[e]de][^ZcghfY_efgfbfdQ^^\bdZaaRMZZT\FRT\LLYYZTGT]_[^a^[^aBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 2:N:0:TAGCTG
 SEQ: ATGTGTCGATGCTGGATAACGAATGGGGTATGTCGGTGTATCCGCTGGGGGCTGGTCATGAAGGGGTGGGGCATATTGCAGCTGTGGGTTCGGGGGCC
 SEQ_LEN: 98
 SCORES: JJ\caa`^Ye`gW^[J[Q[`YJJ`dfa^PYbfX^^_H^^eh]fb`aefGZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 1:N:0:TAGCTG
 SEQ: ATTCCTAACAGTAATATGCAGGATGCCCGCAATACAGATCTGCGTTGGCGCGAGCGTTATCTGTCGGTGTTAGCAGATTTCGTGATGGAGATCGGAAG
 SEQ_LEN: 98
 SCORES: ___cc`Sc^J[ecK``f]cY^RPbcRYJQQY^YccacfehhheU^^^eXFS_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 2:N:0:TAGCTG
 SEQ: CCATCACGCAATCTGCTAACACCGACAGATAACGCTCGCGCCAACGCAGATCTGTATTGCGGGCATCCTGCATATTACTGTTAGGAATAGATCGGAAG
 SEQ_LEN: 98
 SCORES: ZZac^cd`gf`eeifhh`dfbaafagha`g`_`e`a^cZ`edS\deedcc`^_]]bccRTZQW[T^bbb__bbbb__bc]bc_R^bc]_]bbba[[^R
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 1:N:0:TAGCTG
 SEQ: CATAGGCTTTTTTAACGGCCCAGCCAAAGGCGATCAGGCCAAATAGNANTACCCACCAGTACTGTTGCATNGTCTCAGAAATGNNCAATACAAATTGG
 SEQ_LEN: 98
 SCORES: _[_cccccgcaeeaeJb`b^dd_cg]cZedbfU_eghhhddfg[f]BLBLTZ^abbb^aT]b_`]`b`Y`BKT^^ac_YYY_`BBJGQW_b]bbbbbb
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 2:N:0:TAGCTG
 SEQ: CGGCCNNNACCCAATTTGNNTTGGGCATTTCTGANNNNNNNCNACNNTACTGNNGGGTANTGCTNNNTGNNNNGNNNNNNNNNNNNNNNNNNNNNNNN
 SEQ_LEN: 98
 SCORES: WZ^ceBBBQQQQbffgggBBSQ`_fRZdegffdhBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 1:N:0:TAGCTG
 SEQ: GCTTTGACATAGTCGCTCCAGAATTGCCAGCTAGGGTTAGCTTGGCAACTGCAGCGACGTAATGTGCTGTGGCAGATCAATTTATCTGTTTTGAATCA
 SEQ_LEN: 98
 SCORES: ^P^PJ\Y`eea`e[daYdecggadgdXJIYVbdc`efg_cdedI^aXIO^abeb\eL_daQU^_V]``]UGTZ\^BBBBBBBBBBBBBBBBBBBBBBB
+ORDER: paired
 ---
 SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 2:N:0:TAGCTG
 SEQ: GGTTATCGATCTGGAAAAAGCAACTAAACCTAAAGCTAAACCACGTAGCGCCGGGTAAATGATTCAAAACAGATAAATTGATCTGCCACAGCACATTA
 SEQ_LEN: 98
 SCORES: ^VYPJQ`c^JJ[b[efg^dHJ`aa`adXd_ZXXbIIIY[af_H^aWHWPZ[`gggFFZ^bd_Z]Zb_]ba\^ZGY_`TZ``cc[bbR]]^aaXQ[bbb
+ORDER: paired
+---
+SCORES: ffffcfffffded^eddddddbdcdeedcefecfefdffecabccBB`b`
+SEQ: CCNAGGAGGAGNCAATAAGAGACCATTCGTATATGATCTCTCAGGAGAGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1044:7943#TTAGGC/1
+ORDER: orphan 1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNNNNGGNNCNANNANNNNGTNNNTNGNANNNNCNNANTTGNNNNNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1041:14486#TTAGGC/2
+ORDER: orphan 2
 ---