[med-svn] [libssw] 04/07: add testcase for command line tool
Sascha Steinbiss
satta at debian.org
Fri Jun 24 15:03:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository libssw.
commit 9e00be24c9f015c8f2985615c3d7d13fcb1593d2
Author: Sascha Steinbiss <satta at debian.org>
Date: Fri Jun 24 14:56:56 2016 +0000
add testcase for command line tool
---
debian/tests/control | 4 +
debian/tests/run-example | 16 ++
debian/tests/run-example.out | 408 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 428 insertions(+)
diff --git a/debian/tests/control b/debian/tests/control
index 86d24ae..c6c33d1 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -3,3 +3,7 @@ Depends: libssw0, libssw-dev, build-essential, zlib1g-dev
Tests: build-lib-java
Depends: libssw-java, default-jdk-headless
+
+Tests: run-example
+Depends: ssw-align
+Restrictions: allow-stderr
diff --git a/debian/tests/run-example b/debian/tests/run-example
new file mode 100755
index 0000000..3ad8ca7
--- /dev/null
+++ b/debian/tests/run-example
@@ -0,0 +1,16 @@
+#!/bin/sh
+# autopkgtest check: Run test alignment with command line tool
+# Author: Sascha Steinbiss <satta at debian.org>
+set -e
+
+DEMO=$(pwd)/demo
+DEBDIR=$(pwd)/debian
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+
+cp $DEMO/ref.fa $DEMO/1k.fa .
+ssw-align -c ref.fa 1k.fa | tee out
+diff out $DEBDIR/tests/run-example.out
+ssw_test -c ref.fa 1k.fa | tee out
+diff out $DEBDIR/tests/run-example.out
diff --git a/debian/tests/run-example.out b/debian/tests/run-example.out
new file mode 100644
index 0000000..7fedb30
--- /dev/null
+++ b/debian/tests/run-example.out
@@ -0,0 +1,408 @@
+target_name: chr1
+query_name: chr1
+optimal_alignment_score: 2002 suboptimal_alignment_score: 1000 strand: + target_begin: 1 target_end: 1001 query_begin: 1 query_end: 1001
+
+Target: 1 TAAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCAC 60
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 1 TAAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCAC 60
+
+Target: 61 TACACAATTCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGA 120
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 61 TACACAATTCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGA 120
+
+Target: 121 AAACATAGGAAAAAATTATTTAATAATAAAATTTAATTGGCAAAATGAAGGTATGGCTTA 180
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 121 AAACATAGGAAAAAATTATTTAATAATAAAATTTAATTGGCAAAATGAAGGTATGGCTTA 180
+
+Target: 181 TAAGAGTGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACC 240
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 181 TAAGAGTGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACC 240
+
+Target: 241 CAAGGATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTC 300
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 241 CAAGGATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTC 300
+
+Target: 301 ACATGTATTCATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCAT 360
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 301 ACATGTATTCATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCAT 360
+
+Target: 361 AGAACACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATG 420
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 361 AGAACACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATG 420
+
+Target: 421 GTGATTTAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAAC 480
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 421 GTGATTTAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAAC 480
+
+Target: 481 TGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCACT 540
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 481 TGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCACT 540
+
+Target: 541 CCCTCCATAAATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCCTTGCTCTTCTTTCT 600
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 541 CCCTCCATAAATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCCTTGCTCTTCTTTCT 600
+
+Target: 601 CTCCTATTGCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAATAA 660
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 601 CTCCTATTGCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAATAA 660
+
+Target: 661 CAAAATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAG 720
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 661 CAAAATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAG 720
+
+Target: 721 TGGTTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGA 780
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 721 TGGTTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGA 780
+
+Target: 781 GTATATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGAC 840
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 781 GTATATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGAC 840
+
+Target: 841 TTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCT 900
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 841 TTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCT 900
+
+Target: 901 TAATTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTC 960
+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Query: 901 TAATTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTC 960
+
+Target: 961 TAATTTTTCACTTTACATCACATAATGAATGGATCCAAATA 1001
+ |||||||||||||||||||||||||||||||||||||||||
+Query: 961 TAATTTTTCACTTTACATCACATAATGAATGGATCCAAATA 1001
+
+target_name: chr2
+query_name: chr1
+optimal_alignment_score: 312 suboptimal_alignment_score: 311 strand: + target_begin: 4437430 target_end: 4438470 query_begin: 9 query_end: 971
+
+Target: 4437430 TTGATTCCACAGATTCCAATAGAATAGTTTGAAGATGGAACAATTGAGAATTCTGAATGC 4437489
+ ||*||**|***||*********|*|*******|***|*||***|***|*******|****
+Query: 9 TTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCACTACACAAT 68
+
+Target: 4437490 TAAGCTAATTAGATATGTTTTCTTTGAAGGAAAACTACATTGTATTATTTTGCCTCCTCC 4437549
+ |*******||***|*|****|**|||****|******|*|*****|*||******|*|**
+Query: 69 TCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGAAAACATAG 128
+
+Target: 4437550 CTCCTCCTAGAAGCCTTTAAAATTCATGCATCATTTTAAAAGTTTTGAAATTTTTCAAGA 4437609
+ *******|*******|***|||*|************* ******|*****||*|*|***
+Query: 129 GAAAAAATTATTTAATAATAAAATTTAATTGGCAAAA--TGAAGGTATGGCTTATAAGAG 186
+
+Target: 4437610 TTATGTTTAAGTATATTAAATATTTTGTTCAGTCATCCCAATTAGTTTTCAATGGCCCTT 4437669
+ |**|*|***|*|*|*||*|*|*|*****|||*|**||**|||*|*|*****|********
+Query: 187 TGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACCCAAGGA 246
+
+Target: 4437670 TCCATTTAAAGAGTTTGGACATTCCATATAAAAAAGACAATGTCATCTACATTTTCTTTG 4437729
+ |*|**|*|||*****|**|**|**|||*||*|******||****|**|*||||**|*|**
+Query: 247 TTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTCACATGT 306
+
+Target: 4437730 TTTTCTTAATTATATCTTTTCCTTTTTACAAATTTCTTAAAAATAGGTGTAAGATCTCTG 4437789
+ *||**||**||***********|*******|***|**|****|*|**|************
+Query: 307 ATTCATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCATAGAACA 366
+
+Target: 4437790 ATTTAACCTATGTGCGTCTTAATTTTTCAGCTTCTCTGTCATTTTATTAGATGTTTTTAT 4437849
+ ********|*|*|*|*|**|************|*||**|||*|***|*|||****|***|
+Query: 367 CCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATGGTGATT 426
+
+Target: 4437850 TGTTTTTAATTACTAAATTAATCTTAATCTATGCTTATTATATCATTCTCCATTACGTTA 4437909
+ |*********||*||||*|*||***|*******|**|**|*|||**||||*|****||**
+Query: 427 TAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAACTGGTGT 486
+
+Target: 4437910 TGGATACAACAACTTGGTGAATGTTTCTGAGATTAACACTAAAAATATTTAACAATCTCT 4437969
+ **|**********|**|||**|||*|*|*|||***|*|***|*||*||||*||***|||*
+Query: 487 GTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCACTCCCTCC 546
+
+Target: 4437970 CTCATTTTTATCTTTTCTTTCTTTTTCTCTTTGTCTTTCTCACTCTCTATTTATCCTGTT 4438029
+ *|*|*|*|*|***|*|**||*|*|||*||*||**|||||********|*|||*||***|*
+Query: 547 ATAAATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCCTTGCTCTTCTTTCTCTCCTA 606
+
+Target: 4438030 ACATCTTTGCTTCTATCTCTTTCTCTGTTTTTTTTTTTTAATATTTAAATAATGCTTCTG 4438089
+ *****||***|||**|**|||****|**********|***|***|**||*|***|*****
+Query: 607 TTGCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAATAACAAAAT 666
+
+Target: 4438090 TCTGAGGAGGTTAAGAAGTGAAAGAAGACATTGTGAGATGGAGAATCTTTATTAAGATAG 4438149
+ ***||*|***********|*|*|**|****|****|*| |*****||****||**|*|
+Query: 667 ATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAA---ATGCCATTATCCAAAGTGG 723
+
+Target: 4438150 AAGACAAAGAGGGGATGATGTGGACACTTTCAGGATGTGGAATGGTTACATACATTATTC 4438209
+ ****|*|*****|**************|*******|*********||**|***|**|*|*
+Query: 724 TTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGAGTA 783
+
+Target: 4438210 TGTTATCACAAGGTTAGCTAAACTCTCTTTCATAAAATCTCTCTTGTTTCTTACTCCCTA 4438269
+ |*|||****|****||*|**************|****||**|*****||*******|*|*
+Query: 784 TATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTG 843
+
+Target: 4438270 AATCTCAAATAAGTGACTAAAAAATGCCTGGATGACCCCAAACAGTAAGAATAGCTTGTA 4438329
+ ******||***|*******|****************|****|***|***|**|***|**|
+Query: 844 TCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAA 903
+
+Target: 4438330 GGTCTCTGAAGATGTTATCTTTTG-CCCTGGGAAGGTGGATTCCTATACTAACACCTGCA 4438388
+ ***|*|*********|***||*** ***|****|**||*****||**|*|*********|
+Query: 904 TTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTCTAA 963
+
+Target: 4438389 CTTGAAAAGGTGAACAAGATAATTTTGTATTTATTTTCTCACTACCACTGCAGGTAGCAT 4438448
+ *||***|***|**|**|*|||||*******|*****|***********************
+Query: 964 TTTTTCACTTTACATCACATAATGAATGGATCCAAATA 1023
+
+Target: 4438449 GGGACACTTCTTTATTATTCACAAGAAGAGTTGCTTAATTTTTTCGTTTCCTGATGCTTT 4438508
+ ******************** ************************************
+Query: 1024 ---- 1079
+
+Target: 4438509 CAGCATGGCCCCTTTGGCAGAGGACATTTAATTCTTCTGGGCTTCAGGGAACAAAAGTTG 4438568
+ ******************** *************************************
+Query: 1080 --- 1136
+
+Target: 4438569 TGCTTACTTTGCCATTGGAG 4438588
+ ********************
+Query: 1137 1156
+
+target_name: chr3
+query_name: chr1
+optimal_alignment_score: 291 suboptimal_alignment_score: 289 strand: + target_begin: 680970 target_end: 682002 query_begin: 9 query_end: 998
+
+Target: 680970 TTAAATTGTCAACATGGTATATATGAAATGAATTGGGTTTATAATAGTAAACCAATCTTG 681029
+ ||||*****************|||**|**|******||*******|****||*|**|***
+Query: 9 TTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCACTACACAAT 68
+
+Target: 681030 CATTCCTAAAATAAATCCTATTTAGTTATCGTGTGTTATTTTCTTAATACAGTGTTGGAT 681089
+ **|**||****|***|***||*****|*||*|****|*||*|||***|**********|*
+Query: 69 TCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGAAAACATAG 128
+
+Target: 681090 TAAGTTTGCTATTTTTTATTTTAAAATTTTACATTATTTTCTTCAGTGATATTGACCTGT 681149
+ *||********||**|*||***|***** *|*******|**||**||**********
+Query: 129 GAAAAAATTATTTAATAATAAAATTTAA----TTGGCAAAATGAAGGTATGGCTTATAAG 184
+
+Target: 681150 AGTTTTCTTTCATTATACTGTTTTATCAGATTTAGGTATCAGTGTTATAGTTTCTTCATG 681209
+ |||*||*|***|||*|**|***|*******|****||***|******|*|******||*|
+Query: 185 AGTGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACCCAAG 244
+
+Target: 681210 AAAGGAATTAAGATGTTTTCCTTCCCTTTCAATGTTCTGAATAATCATACAGCATTATGA 681269
+ *|*****|*||******|*|**|*****|**||*|||***|*****|*|*****|*|***
+Query: 245 GATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTCACAT 304
+
+Target: 681270 CTATCTGCCATTTAAATCTTTAGAATAATTACCTTGTGAAACTATGTGGGCTTGGTGCTA 681329
+ *|||******|||********|*******|******|*****|************|***|
+Query: 305 GTATTCATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCATAGAA 364
+
+Target: 681330 TTTTGTGTAGTATTTATCTAATTGTTTCCTATATTTCTTCTATGAAATTGGTTGATTTAA 681389
+ ******|***|*|||***||||*****|****|*|*****|****|||||*******|*|
+Query: 365 CACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATGGTGA 424
+
+Target: 681390 TCTTTCTAACACTAATAAGATTAATTTGAGTAAACTTCATTTCTCTAGAAAATAATTAAT 681449
+ |*|**|*||***||||||**|||********|**|**||***|****|****|||*|**|
+Query: 425 TTTAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAACTGGT 484
+
+Target: 681450 TCATCAAATTAAATCAAATTTGAAATTTGATTTCAAATTTATTTGTGTCAAAGTAAAGGA 681509
+ ***|*****|***|*****|*****|*||***************|***************
+Query: 485 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCACTCCCT 544
+
+Target: 681510 GGTTTCCTGTCATTTTAAAATTCTCTGTTGTTTTAATAGTAACTTGTTTCTTATTATTTA 681569
+ ***|***|*|||***||***||*|||*||***||*****|***|**|*|**|*|***|**
+Query: 545 CCATAAATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCCTTGCTCTTCTTTCTCTCC 604
+
+Target: 681570 TAACTTTATATATTTGTACTTTTTCCTTTTTTATCAAATGAACTGAGTTTTAACATCGCA 681629
+ ||****|*|***||**|****||**|*|*******||||*|****|*****||*|* **|
+Query: 605 TATTGCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAATAA-CAA 663
+
+Target: 681630 TTTAATTTTAATTATCTAATCTAAATCTAAAAGCTGATATTTGATTCAATTGTCAGAAAT 681689
+ **||****|**|*|*|***|*|||***|||*******||***********|***|*****
+Query: 664 AATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAGTGG 723
+
+Target: 681690 CTCTTAAGTATATTGGGATCAACTTGGAAAAGTAAATTGACTTTAAACAGTACACTTTAT 681749
+ *|||**||*******|****|**|****|*|*****|**|*|*||**||****|******
+Query: 724 TTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGAGTA 783
+
+Target: 681750 GAACTTTAAATTACAGATCAGATATTTTTAGTAAAATTTTATCCAAACTAAGATGCAATA 681809
+ *|******||********|***|*|****|*******|***|***||*|*|***|***|*
+Query: 784 TATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTG 843
+
+Target: 681810 TGAGTATAATCACTGATTCAAAAAGCTTCCTTTAGTGAGCATGAAATATCTCACTATTTT 681869
+ |*|**|*|***|****|**|*******|**|*****************|*|*|*|*||**
+Query: 844 TCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAA 903
+
+Target: 681870 AATTTTAATATTGATTGTGTGTTAAA--ATAATAATAATTGCATTATATTATTGATAATG 681927
+ ********|**||**|***|*****| *|***|****|**|**|**|*|*|***|****
+Query: 904 TTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTCTAA 963
+
+Target: 681928 TGTATTCTTGTCATGTTTCCATTCTTACTGGAAATGCCTCCAGTGTTTCTCCATCAAATA 681987
+ |*|*|***|*|*********|*|**********|*************************
+Query: 964 TTTTTCACTTTACATCACATAATGAATGGATCCAAATA - 1022
+
+Target: 681988 GTATACTGGCTCTAAGACTAATTTAAAGGACAAGATGGCCAACTAGACACAGCCAGGAAG 682047
+ ***********************************************************
+Query: 1023 - 1081
+
+Target: 682048 CACTGTTCCTACCCCCAAAAGACCAAAGTTTCAAGTAAACCAACATAACTTGGACAGATC 682107
+ ************** *******************************************
+Query: 1082 --- 1138
+
+Target: 682108 TTCAAAGAGAAAATGCCCAGTGGATGAAGATGTGAT 682143
+ ************************************
+Query: 1139 1174
+
+target_name: chr4
+query_name: chr1
+optimal_alignment_score: 280 suboptimal_alignment_score: 273 strand: + target_begin: 47000 target_end: 48059 query_begin: 2 query_end: 1001
+
+Target: 47000 AAACATCTTATAGCTACTGGATTCTTTTTTGCCTATGTATTTATATATGTGCTGTATCTA 47059
+ |||||**|||********|***|**|**|*******||***||***|*************
+Query: 2 AAACAGGTTAATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCACT 61
+
+Target: 47060 TGTAATGTCTATTTTTATAAAGCTCTAATTGACCTAGAGGAAAATGAGTTTTTGAATCAA 47119
+ ****|**||||**|||**********|*******|**|***|******|*|*|** *|
+Query: 62 ACACAATTCTAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTT---TA 118
+
+Target: 47120 ATATTTTTTGAAGGGAAAGTAAAAACTGTGGTACATTGAAGTTCACATGACTAATCATTG 47179
+ **|****|*|*|***||******||***|***|**|****|***|*||||**********
+Query: 119 GAAAACATAGGAAAAAATTATTTAATAATAAAATTTAATTGGCAAAATGAAGGTATGGCT 178
+
+Target: 47180 AGAAATAAAAACAGACTTAGCAATTATTGGTAAAAAGCAGATGTTAAAATATACATTTTT 47239
+ ***||*|********||******||****|||**|**||****|**|||||*********
+Query: 179 TATAAGAGTGTTTTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACA 238
+
+Target: 47240 GTTCAGGGTTAAAGGATTGTTCTGAATTAGATAAGATAAAGCTAAAAGTTTAAACAAGTT 47299
+ ****|||*||*****|*****|********||*|**||*|******|**|*|||*****|
+Query: 239 CCCAAGGATTCTGTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCAT 298
+
+Target: 47300 ATAAAAAGTTTCTATAAAATTCATCTTGCCAAAGAAATTTTGTCCATGAACATTAAATTA 47359
+ **|*|****|||**|****|**|********|**|**|****|*|**|***|********
+Query: 299 TCACATGTATTCATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGC 358
+
+Target: 47360 CGAAAGGTATTATATGTTTTTTTGGTAAATTAAGCATTTAAATAATAGCACAACAAGGTA 47419
+ **|*|*********|*||||||****|********||*****|*||*****||****|*|
+Query: 359 ATAGAACACCCGGGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAA 418
+
+Target: 47420 CTCTTAAGGCACTAATCTGCTCTTTAGCAAAATTTGTAAAGTGTTATAAACGGGTTTTAC 47479
+ ***|*|****||*||*************|**|*****|*******|*|*|***||*|***
+Query: 419 TGGTGATTTAACAAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTA 478
+
+Target: 47480 TTTTGTAAATTTTTTGAAACAATTGTGGCAAAATAAATAACATGGTAATCTGGAATTCTA 47539
+ **|*||***|*|*|*********||||******|**|**|****|**|*****||||**|
+Query: 479 ACTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCA 538
+
+Target: 47540 TTTCATAACATCAAGTGTTTTAAACCTCTAACATTTCTTCCCAAAATCAAACTTCAGTTT 47599
+ *|*|*|******|**|******|**||*|****||||*|**|*****|***||****|||
+Query: 539 CTCCCTCCATAAATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCCTTGCTCTTCTTT 598
+
+Target: 47600 CAAAATTGTCTTTCCTCGTGCCTGACTTTTGAATGCTACAGAGGGCCCCTGGAGTATCCA 47659
+ |*****|*|***|***|*|*|*|**|*||***||***|*|*|*****|*******|****
+Query: 599 CTCTCCTATTGCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAAT 658
+
+Target: 47660 AAAGAGAGGTAAACTGGATTATTTGACATATTTAGTTACATG--GGATTGCCAATCTTCT 47717
+ ||**|*|**||*|**|******||***|***|||*****|** **||**|*********
+Query: 659 AACAAAATATAGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAA 718
+
+Target: 47718 TTAGGTTATATAGGTTATATTTTGATAAATATTCTATAGGTTATATTTTGATAAATGATA 47777
+ ***||||*|*|||******|**||***|***||**|||**|||*|*|*|**|*||**|*|
+Query: 719 AGTGGTTCTCTAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAA 778
+
+Target: 47778 CTAATATATGTTCCAAAATTGTATGAGATTTCTAATGTCTGAGTATATGCTATCAAAATT 47837
+ ********|*****|*|**|*|*******|****|**|*|****||***|*||**|****
+Query: 779 GAGTATATTACATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGG 838
+
+Target: 47838 AAGGTTTTTATGTTAAGTTATTGTAAACCACAGAGATTATCAAACTTCTTTGTCAACTGT 47897
+ |****|***************||||******|*|*****|********||||**|****|
+Query: 839 ACTTGTCAACAAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAAT 898
+
+Target: 47898 GTTTCTGACTATAACTACCCTGGACATTTTGTTATTCAAAGACAATTGTCTTGTTTAGAT 47957
+ *||**|*||*********|*|*******|**||*|***|***********|***|****|
+Query: 899 CTTAATTACCCCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACT 958
+
+Target: 47958 CCTTTTCAAGAGATAGTTTATAAGAAGCTACAGAACTGTGACAGGTGCTCTCAAATGCAG 48017
+ *||**|*******|*******|***|* |**|****|***|*******************
+Query: 959 TCTAATTTTTCACTTTACATCACATAA-TGAATGGATCCAAATA 1017
+
+Target: 48018 TTTTCCAAATAACTTTGGAGATCATGACATTGAAATAAAGTAAAACATACAAGACTCATG 48077
+ ************************************************************
+Query: 1018 1077
+
+Target: 48078 AAGAGCTAAAATGTTCACAAATATCAAGCAGAACAAGGGTTAACTAAATGGACTGAACTA 48137
+ ***************************** ******************************
+Query: 1078 - 1136
+
+Target: 48138 ATAGAAAACTGAAATATTTTTTTTTTACTTATGGTTGGACGATTGCTGATTCTTGTTTTG 48197
+ *********************** ***********************************
+Query: 1137 -- 1194
+
+Target: 48198 TTTTTCAGAGTCAAGG 48213
+ ****************
+Query: 1195 1210
+
+target_name: chr5
+query_name: chr1
+optimal_alignment_score: 230 suboptimal_alignment_score: 199 strand: + target_begin: 8806 target_end: 9723 query_begin: 11 query_end: 974
+
+Target: 8806 AATGGCCAGGGCACTGAGGAGCTGTGGAAGAACTGGGGAAATCACCGAAACCCAGTACCA 8865
+ |||*||||*|*||**|**|***|**|****|***|******|*|****|***||**|***
+Query: 11 AATCGCCACGACATAGTAGTATTTAGAGTTACTAGTAAGCCTGATGCCACTACACAATTC 70
+
+Target: 8866 TTTCAGTGAGGCCATTCTCCA--AAAACTCTCTCCATCTTATTTCTTGGGGAAAGAGTTC 8923
+ |**|**|*************| ****|**||****|**|*|*|*||*|**||*******
+Query: 71 TAGCTTTTCTCTTTAGGATGATTGTTTCATTCAGTCTTATCTCTTTTAGAAAACATAGGA 130
+
+Target: 8924 TTCTACTTACAATATGATCAACCTGATTAAGAATATATTGGTTTCTATAACTGTGATGCA 8983
+ ****|*|****|*******||**|*|||***||*||***|||*|***|*|******||**
+Query: 131 AAAAATTATTTAATAATAAAATTTAATTGGCAAAATGAAGGTATGGCTTATAAGAGTGTT 190
+
+Target: 8984 GATTATAACTATACAAATGCCAATTACCAGAAGCTAAGCCACCCTGATTCCAAAATATAG 9043
+ *********|*|*||*******|*|**|*|*****||************||||****|**
+Query: 191 TTCCTATTGTTTTCAGTGTAGGACTCACTGTTCTAAATAACTGGGACACCCAAGGATTCT 250
+
+Target: 9044 TCTCACATTTCATGGTTTCCTGGTATCAGAAATCCCTATGAGCCTGAGATTTTTTCCCTT 9103
+ ****|***********||*****|***|************|***|*|******|****|*
+Query: 251 GTAAAATGCCATCCAGTTATCATTTATATTCCCTAACTCAAAATTCATTCACATGTATTC 310
+
+Target: 9104 AAAGCAAATACTGAAGATAAGAAACCAATTAATTTCATTGTTGCTATCTTGTATCCAATG 9163
+ |*************|*||*||*|***|******|***|******|**|*|**|*|****|
+Query: 311 ATTTTTTTCTAAACAAATTAGCATGTAGAATTCTGGTTAAAATTTGGCATAGAACACCCG 370
+
+Target: 9164 GCATAAAATCTATACTAACTTGATTAGAAATTCTGCCAATGAACAACTTTATTGTTTTGA 9223
+ |*******|**|||*|******|*||****|**|*|********|***|**|**|||***
+Query: 371 GGTATTTTTTCATAATGCACCCAATAACTGTCATTCACTAATTGAGAATGGTGATTTAAC 430
+
+Target: 9224 GTGATGAAGCCCCATTTGAGAATATAGGCTCAATGGCCTTGCTCTTAACTGTTCTCTATG 9283
+ *******|******||****||***|*||***|***|*|***|||**|************
+Query: 431 AAAGGATAATAAAGTTATGAAACCAATGCCACAAAACATCTGTCTCTAACTGGTGTGTGT 490
+
+Target: 9284 CAGTCACTTTCTTCTGCACTAAAGTGCCAATACAGATACTGAATACATTGATTTAAATAC 9343
+ **||***|*|*|*******|***********|*|||*|***|||*********|**|||*
+Query: 491 GTGTGTGTGTGTGTGTGTGTGTGTAAGAGGGAGAGAGAGAAAATTTCACTCCCTCCATAA 550
+
+Target: 9344 ATAGATATATAAATAGATATTTAAATATGCAATATATATGGATACTTTATATATTGATTT 9403
+ ||*******||******|*|||*****|*|**|*** |*|*|**|*|*|*|*|****||
+Query: 551 ATCTCACAGTATTCTTTTCTTTTTCCTTTCCTTTCC--TTGCTCTTCTTTCTCTCCTATT 608
+
+Target: 9404 AAACATTTTCCTCTCATAGATGAAAAATCACTCTAACATGTATTGATGGCTTCACAAGAA 9463
+ *******||*|**|******|*|*|||**|*****|****|||*||******||*||*|*
+Query: 609 GCTTTCCTTTCATTTCCTTCTCATAAAAGAAAAATAACAATATAGAAAATAACAAAATAT 668
+
+Target: 9464 ATCATTTACAGAAAATAATTGCATATGATACAGTGTTTGTGCCAAAATGTATTCATGGCT 9523
+ |*****|**|*****|*|*|****|*|*|||******||*****|*****|*|**|****
+Query: 669 AGATGGTCAACCTTTTTAATATTAAGGTTACCTAAAATGCCATTATCCAAAGTGGTTCTC 728
+
+Target: 9524 TTAAAAACTTCAGTGGAAATGTCTATTCAGATCCCTAGCCCATTGTTAAATTGGTTTCTG 9583
+ |**|*|***|*|*****|***|****|****|*|***|********||||**|**|**|*
+Query: 729 TAGAGATGCTGATGTATATACTTACATATTTTACAGTGTATTCAAATAAAGAGTATATTA 788
+
+Target: 9584 TTTTCTTGCTAAGTTTGAGCTGCTTATAGATGATGGATATTGACC-CCTTATAGATGTTG 9642
+ **|******||***||**|***|**|****||******|****** |***|****|****
+Query: 789 CATAAGACATATCCTTTTGTAACCAACTTTTGTCATTAACAATTTACTGGACTTGTCAAC 848
+
+Target: 9643 GATATTGACCCCTTGTGGATGTATGGCCGGTGCTTTTCCCAGTATTTAGGTCATCTCTGC 9702
+ *|***|*|**|**|*|*|***************||******|***|*|*******|***|
+Query: 849 AAACCTAAATCTGTATCGTCTATAATGGCTACGTTCATTTTGGTATGAATCTTAATTACC 908
+
+Target: 9703 ACACTGTTGATTGTTTCCTTTGCTGGGTAGAAGTTTTTTGGTTTGATGTAATCCTATTTG 9762
+ *|**|*|**|||*|||**|****|****|*|*||***|********|*********|||*
+Query: 909 CCTTTCTGCATTATTTAATGATTTTCTCATATGTCACTCTTAAATGTACTTCTAATTTTT 968
+
+Target: 9763 TTTAGTTTTACTTTTGTTGCTTGCACTTTTGGTGTTAAGTCCAAAAGAAAATTGCAAACA 9822
+ *****|****|***|**| *******|*****|*************************
+Query: 969 CACTTTACATCACATAAT---GAATGGATCCAAATA 1025
+
+Target: 9823 CCAATGTCGTGTAATTTTTACTCTCTGTTTTCTTCTGGTAGTTTTAGAGCAAGTTTATCC 9882
+ ************* **********************************************
+Query: 1026 - 1084
+
+Target: 9883 AACCTGTGGTCTGTGGGC 9900
+ ******************
+Query: 1085 1102
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libssw.git
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