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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/commit/8c33f70533310cf602c9028e42994a262987a36a">8c33f705</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-04-17T22:55:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extending support for Python files of hisat2
bcbio needs them to build-testing
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#071dad660b510ffd881faa8d772f1c80d774a784">
debian/install
→
debian/hisat2.install
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hisat2/commit/8c33f70533310cf602c9028e42994a262987a36a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,6 +2,11 @@ hisat2 (2.1.0-3) UNRELEASED; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Install hisat2_extract_splice_sites.py</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Separated series of .py scripts and modules into separate</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3-hisat2 package.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 25 Mar 2019 11:35:33 +0100</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">hisat2 (2.1.0-2) unstable; urgency=medium</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hisat2/commit/8c33f70533310cf602c9028e42994a262987a36a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="diff-line-num unfold js-unfold new_line" data-linenumber="16" 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">@@ -16,8 +16,8 @@ Package: hisat2</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: amd64 kfreebsd-amd64</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> ${perl:Depends}<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right"> python</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ${perl:Depends}</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">Recommends: python3-hisat2</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Description: graph-based alignment of short nucleotide reads to many genomes</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> HISAT2 is a fast and sensitive alignment program for mapping next-generation</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> sequencing reads (both DNA and RNA) to a population of human genomes (as well</span>
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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">@@ -30,3 +30,24 @@ Description: graph-based alignment of short nucleotide reads to many genomes</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> indexes), combined with several alignment strategies, enable rapid and</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> accurate alignment of sequencing reads. This new indexing scheme is called a</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> Hierarchical Graph FM index (HGFM). </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Package: python3-hisat2</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> hisat2,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> python</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Description: Python scripts accompanying hisat2</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> HISAT2 is a fast and sensitive alignment program for mapping next-generation</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> sequencing reads (both DNA and RNA) to a population of human genomes (as well</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> as against a single reference genome). Based on an extension of BWT for graphs</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> a graph FM index (GFM) was designed and implementd. In addition to using</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> one global GFM index that represents a population of human genomes, HISAT2</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> uses a large set of small GFM indexes that collectively cover the whole genome</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> (each index representing a genomic region of 56 Kbp, with 55,000 indexes</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> needed to cover the human population). These small indexes (called local</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> indexes), combined with several alignment strategies, enable rapid and</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> accurate alignment of sequencing reads. This new indexing scheme is called a</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> Hierarchical Graph FM index (HGFM). </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> This package provides a serires of platform-independent scripts that are typically</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> expected to be co-installed with the hisat2 binary.</span></pre>
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<li id="071dad660b510ffd881faa8d772f1c80d774a784">
<a href="https://salsa.debian.org/med-team/hisat2/commit/8c33f70533310cf602c9028e42994a262987a36a#071dad660b510ffd881faa8d772f1c80d774a784"><strong>debian/install</strong>
→
<strong>debian/hisat2.install</strong>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">hisat2</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">hisat2_extract_splice_sites /usr/bin</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">hisat2</span><span class="o" style="font-weight: 600;">-</span><span class="nx">build</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">hisat2</span><span class="o" style="font-weight: 600;">-</span><span class="nx">build</span><span class="o" style="font-weight: 600;">-</span><span class="nx">s</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">hisat2</span><span class="o" style="font-weight: 600;">-</span><span class="nx">build</span><span class="o" style="font-weight: 600;">-</span><span class="nx">l</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span></span>
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