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commit 9e00be24c9f015c8f2985615c3d7d13fcb1593d2 Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
