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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/kmer">Debian Med / kmer</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/kmer/-/commit/81d0ff4a890f296b8a02aa31baf2689293a1e005">81d0ff4a</a></strong>
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<span>by Antoni Villalonga</span>
<i>at 2020-04-19T10:11:50+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updated spelling.patch & d/upstream/metadata: Repository and Bug
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7e6aed1a543f8988c3231e7ea0eed4ecabdc9a7c">
debian/man/leaff/leaff.1
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<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
debian/patches/spelling.patch
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kmer/-/commit/81d0ff4a890f296b8a02aa31baf2689293a1e005#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kmer (0~20150903+r2013-8) UNRELEASED; urgency=medium</span>
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<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"> * Team upload.</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"> [ Antoni Villalonga ]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/upstream/metadata: Repository and Bug</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Updated spelling.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">-- Antoni Villalonga <ntoni@friki.cat> Sat, 19 Apr 2020 17:59:48 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">kmer (0~20150903+r2013-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/kmer/-/commit/81d0ff4a890f296b8a02aa31baf2689293a1e005#7e6aed1a543f8988c3231e7ea0eed4ecabdc9a7c"><strong>debian/man/leaff/leaff.1</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">@@ -72,7 +72,7 @@ ANALYSIS FUNCTIONS</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> --partitionmap [ n[gmk]bp | n ] a.fasta</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> Partition the sequences into roughly equal size pieces of</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> size nbp, nkbp, nmbp or ngbp; or into n roughly equal sized</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> par<span class="idiff left right">i</span>titions. Sequences larger that the partition size are</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> partitions. Sequences larger that the partition size are</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> in a partition by themself. --partitionmap writes a</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> description of the partition to stdout; --partiton creates</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> a fasta file 'prefix-###.fasta' for each partition.</span>
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<a href="https://salsa.debian.org/med-team/kmer/-/commit/81d0ff4a890f296b8a02aa31baf2689293a1e005#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Fix spelling</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: S<span class="idiff left right">un, 05 Aug 2018 05:47:52</span> +0200</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org><span class="idiff left right">, Antoni Villalonga <antoni@friki.cat></span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: S<span class="idiff left right">at, 11 Apr 2020 22:30:00</span> +0200</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/libutil/bitPackedFile.C</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libutil/bitPackedFile.C</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -157,7 +157,7 @@</span><span class="idiff left right"> bitPackedFile::bitPackedFile(char const</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -157,7 +157,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> } else if ((at == uint64Swap(ac)) && (bt == uint64Swap(bc))) {</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> endianess_flipped = true;</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> } else {</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">@@ -15,7 +15,7 @@ Last-Update: Sun, 05 Aug 2018 05:47:52 +0200</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libkmer/driver-existDB.C</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libkmer/driver-existDB.C</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span><span class="idiff left right"> const char *usage =</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> " -testexhaustive some.fasta some.meryl\n"</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> " -- Build an existDB table from some.fasta, check _EVERY_ mer\n"</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">@@ -26,7 +26,7 @@ Last-Update: Sun, 05 Aug 2018 05:47:52 +0200</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> "\n";</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libutil/palloc.c</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libutil/palloc.c</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -133,7 +133,7 @@</span><span class="idiff left right"> palloc2(size_t size, void *handle) {</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -133,7 +133,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> root->_cn = root->_nl;</span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> if (root->_dbg > 0)</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">@@ -37,7 +37,7 @@ Last-Update: Sun, 05 Aug 2018 05:47:52 +0200</td>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> root->_cn->_dt = (char *)really_allocate(root->_bs);</span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/sim4dbutils/parseSNP.C</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/sim4dbutils/parseSNP.C</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="p">@@ -491,7 +491,7 @@</span><span class="idiff left right"> main(int argc, char **argv) {</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -491,7 +491,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> fprintf(stderr, " default, and if posTag is not found.\n");</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> fprintf(stderr, "\n");</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> fprintf(stderr, " TAGS: The number immediately after the first\n");</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">@@ -46,3 +46,14 @@ Last-Update: Sun, 05 Aug 2018 05:47:52 +0200</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> fprintf(stderr, "\n");</span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> fprintf(stderr, " -o offset An additive offset to the SNP position.\n");</span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> fprintf(stderr, " The default is 0.\n");</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/leaff/leaff.C</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/leaff/leaff.C</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -126,7 +126,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> fprintf(stderr, " --partitionmap [ n[gmk]bp | n ] a.fasta\n");</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> fprintf(stderr, " Partition the sequences into roughly equal size pieces of\n");</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> fprintf(stderr, " size nbp, nkbp, nmbp or ngbp; or into n roughly equal sized\n");</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf(stderr, " parititions. Sequences larger that the partition size are\n");</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, " partitions. Sequences larger that the partition size are\n");</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> fprintf(stderr, " in a partition by themself. --partitionmap writes a\n");</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> fprintf(stderr, " description of the partition to stdout; --partiton creates\n");</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> fprintf(stderr, " a fasta file 'prefix-###.fasta' for each partition.\n");</span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/-/commit/81d0ff4a890f296b8a02aa31baf2689293a1e005#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -42,3 +42,7 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> Entry: atac</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> Entry: atac, meryl</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Repository: svn://svn.code.sf.net/p/kmer/code/trunk</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Repository-Browse: https://sourceforge.net/p/kmer/code/HEAD/tree/</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Bug-Database: https://sourceforge.net/p/kmer/bugs/</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Bug-Submit: https://sourceforge.net/p/kmer/bugs/new/</span></pre>
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