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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/genomethreader">Debian Med / genomethreader</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/a9650b35a58c075831ff1ba4a68ced69135a4111">a9650b35</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-01T15:48:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">create all BSSM files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/3eb9fa4892fb404eb2a1bfca5cc647fabea8c561">3eb9fa48</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-01T15:50:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">re-enable tests requiring human.bssm
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
debian/patches/debian-gt-libs.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#01d7ada4b7ac538c066cc0213a81ccb823ec2cd4">
<span class="deleted-file">
−
debian/patches/skip-human-bssm-tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561#f19f900306f42aafd11c9c6fd4e4e288988b9c4a"><strong>debian/patches/debian-gt-libs.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -164,3 +164,15 @@</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="diff"> -MT $@</span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> obj/src/core/versionfunc.o: obj/gth_config.h</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -508,9 +505,9 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> -gtdonor -agacceptor -gzip</span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> @touch $@</span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-obj/old_train: ../genometools/bin/gt</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+obj/old_train:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> @echo "[write old BSSMs]"</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @../genometools/bin/gt dev gthmkbssmfiles bin/bssm</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @gt dev gthmkbssmfiles bin/bssm</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> @touch $@</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> obj/gthdata:</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">debian-gt-libs.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">gt-path-fix.patch</span></pre>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">skip-human-bssm-tests.patch</span></pre>
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<li id="01d7ada4b7ac538c066cc0213a81ccb823ec2cd4">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561#01d7ada4b7ac538c066cc0213a81ccb823ec2cd4"><strong>debian/patches/skip-human-bssm-tests.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/testsuite/gth_include.rb</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/testsuite/gth_include.rb</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -111,28 +111,28 @@</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> Name "gth regression test (-exondistri)"</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> Keywords "gth"</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> Test do</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -exondistri"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -exondistri"</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> grep($last_stdout, /length distribution of all exons/)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> Name "gth regression test (-introndistri)"</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> Keywords "gth"</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> Test do</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -introndistri"</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -introndistri"</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> grep($last_stdout, /length distribution of all introns/)</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> Name "gth regression test (-refseqcovdistri)"</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> Keywords "gth"</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> Test do</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -refseqcovdistri"</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -refseqcovdistri"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> grep($last_stdout, /reference sequence coverage distribution/)</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> Name "gth regression test (all distributions)"</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> Keywords "gth"</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> Test do</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -exondistri -introndistri -refseqcovdistri"</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -exondistri -introndistri -refseqcovdistri"</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> grep($last_stdout, /length distribution of all exons/)</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> grep($last_stdout, /length distribution of all introns/)</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> grep($last_stdout, /reference sequence coverage distribution/)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="p">@@ -141,8 +141,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> Name "gth regression test (-skipindexcheck)"</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> Keywords "gth"</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> Test do</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -createindicesonly"</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -skipindexcheck | grep -v -e '^\\$' -e 'file='"</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -createindicesonly"</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -skipindexcheck | grep -v -e '^\\$' -e 'file='"</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/single_exon.out"</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="p">@@ -153,7 +153,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> FileUtils.cp("#{$testdata}gth/genomic_sequence_single_exon.fas", ".")</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> FileUtils.cp("#{$testdata}gth/cdna_sequence_single_exon.fas", ".")</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> # run gth</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species human"</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species arabidopsis"</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> # make sure index files have been created & save mtimes</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> mtimes = {}</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> file_exists("cdna_sequence_single_exon.fas.dna.al1", mtimes)</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="p">@@ -175,7 +175,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> file_exists("genomic_sequence_single_exon.fas.dna.suf", mtimes)</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> file_exists("genomic_sequence_single_exon.fas.dna.tis", mtimes)</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> # run gth again</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species human"</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species arabidopsis"</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> # make sure index files have have not changed</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> cmp_mtimes("cdna_sequence_single_exon.fas.dna.al1", mtimes)</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> cmp_mtimes("cdna_sequence_single_exon.fas.dna.des", mtimes)</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="p">@@ -288,15 +288,16 @@</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> grep($last_stderr, /Illegal character 'x' in file/);</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> end</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Name "align_dna"</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Keywords "gth align_dna"</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Test do</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}align_dna " +</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "#{$testdata}gth/genomic_sequence_single_exon.fas " +</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "#{$testdata}gth/cdna_sequence_single_exon.fas"</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run "grep -v -e '^Genomic Template:' -e 'EST Sequence:' #{$last_stdout}"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/align_dna.out"</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-end</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# has human BSSM (missing) hardcoded into tool</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Name "align_dna"</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Keywords "gth align_dna"</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Test do</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run_test "#{$bin}align_dna " +</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "#{$testdata}gth/genomic_sequence_single_exon.fas " +</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "#{$testdata}gth/cdna_sequence_single_exon.fas"</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run "grep -v -e '^Genomic Template:' -e 'EST Sequence:' #{$last_stdout}"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/align_dna.out"</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#end</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> Name "gth -gff3descranges (single exon)"</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> Keywords "gth gff3descranges"</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="p">@@ -329,7 +330,7 @@</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> Name "gth (detect small initial exon)"</span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"> Keywords "gth gencode"</span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"> Test do</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -species human -exdrop 1 -minmatchlen 12 " +</span></span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -species arabidopsis -exdrop 1 -minmatchlen 12 " +</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> "-seedlength 12 -fragweightfactor 0.5 -introncutout " +</span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"> "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +</span>
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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> "-skipalignmentout -genomic #{$gthtestdata}gencode/ENr233.fa.gz " +</span>
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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="p">@@ -342,7 +343,7 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> Name "gth (detect small terminal exon)"</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"> Keywords "gth gencode"</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"> Test do</span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -species human -exdrop 1 -minmatchlen 12 " +</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -species arabidopsis -exdrop 1 -minmatchlen 12 " +</span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"> "-seedlength 12 -fragweightfactor 0.5 -introncutout " +</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> "-skipalignmentout -genomic #{$gthtestdata}gencode/ENm005.fa.gz " +</span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="p">@@ -355,7 +356,7 @@</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"> Name "gth (detect small exon bug 1)"</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"> Keywords "gth gencode"</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"> Test do</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gth -species human -exdrop 2 -minmatchlen 12 " +</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run_test "#{$bin}gth -species arabidopsis -exdrop 2 -minmatchlen 12 " +</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> "-maskpolyatails -noicinintroncheck " +</span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"> "-seedlength 12 -fragweightfactor 0.5 -introncutout " +</span>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="p">@@ -369,7 +370,7 @@</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"> run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +</span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"> "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +</span>
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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"> "-noicinintroncheck -detectsmallexons -introncutout " +</span>
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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "-maskpolyatails -species human -genomic " +</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-maskpolyatails -species arabidopsis -genomic " +</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> "#{$gthtestdata}gencode/ENm003.fa.gz " +</span>
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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"> "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_2_cdna.fas",</span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"> :maxtime => 900)</span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="p">@@ -381,7 +382,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"> run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"> "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"> "-noicinintroncheck -detectsmallexons -introncutout " +</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "-maskpolyatails -species human -genomic " +</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-maskpolyatails -species arabidopsis -genomic " +</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"> "#{$gthtestdata}gencode/ENm004.fa.gz " +</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"> "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_3_cdna.fas",</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"> :maxtime => 300)</span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="p">@@ -393,7 +394,7 @@</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"> run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"> "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"> "-noicinintroncheck -detectsmallexons -introncutout " +</span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "-maskpolyatails -species human -genomic " +</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-maskpolyatails -species arabidopsis -genomic " +</span></span>
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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"> "#{$gthtestdata}gencode/ENm004.fa.gz " +</span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"> "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_4_cdna.fas",</span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"> :maxtime => 300)</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="p">@@ -405,7 +406,7 @@</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"> run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"> "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +</span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"> "-noicinintroncheck -detectsmallexons -introncutout " +</span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "-maskpolyatails -species human -genomic " +</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "-maskpolyatails -species arabidopsis -genomic " +</span></span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> "#{$gthtestdata}gencode/ENm014.fa.gz " +</span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"> "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_5_cdna.fas",</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"> :maxtime => 600)</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/testsuite/gthbssmfileinfo_include.rb</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/testsuite/gthbssmfileinfo_include.rb</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="p">@@ -5,9 +5,10 @@</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/arabidopsis.out"</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> end</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Name "gthbssmfileinfo (human)"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Keywords "gthbssmfileinfo"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Test do</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gthbssmfileinfo human"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/human.out"</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-end</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# human BSSM file is missing</span></span>
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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Name "gthbssmfileinfo (human)"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Keywords "gthbssmfileinfo"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Test do</span></span>
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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run_test "#{$bin}gthbssmfileinfo human"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/human.out"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#end</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/testsuite/gthbssmprint_include.rb</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/testsuite/gthbssmprint_include.rb</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="p">@@ -5,9 +5,10 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"> run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/arabidopsis.out"</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"> end</span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Name "gthbssmprint (human)"</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Keywords "gthbssmprint"</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Test do</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run_test "#{$bin}gthbssmprint human.bssm"</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/human.out"</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-end</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# human BSSM is missing</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Name "gthbssmprint (human)"</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Keywords "gthbssmprint"</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Test do</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run_test "#{$bin}gthbssmprint human.bssm"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/human.out"</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#end</span></span></pre>
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<a href="https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,8 +13,7 @@ override_dh_clean:</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_build:</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> make licensemanager=no opt=yes 64bit=yes</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> make licensemanager=no opt=yes 64bit=yes obj/train</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> make licensemanager=no opt=yes 64bit=yes obj/gthdata</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> make licensemanager=no opt=yes 64bit=yes train</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> mv bin/bssm debian/bssm</span>
</pre>
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