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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/hts-nim-tools">Debian Med / hts-nim-tools</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c">bf3cc1e9</a></strong>
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<span>by Steffen Möller</span>
<i>at 2020-11-07T20:31:53+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ready for peer review
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#1ec66a592180b9e816019238bbe6d40c69baa20e">
<span class="new-file">
+
debian/patches/import_random.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,6 +2,4 @@ hts-nim-tools (0.2.0-1) UNRELEASED; urgency=medium</td>
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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"> * Initial release (Closes: #973650)</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"> Misses brentp's nim modules lapper and kexec</span>
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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="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 02 Nov 2020 20:26:54 +0100</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: hts-nim-tools</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Maintainer: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> nim,</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> nim-hts-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> nim-docopt-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> nim-unicodedb-dev,</span>
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<td class="diff-line-num new_line" data-linenumber="11" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> nim-unicodeplus-dev,</span>
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11
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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC11" class="line" lang="plaintext"> nim-regex-dev</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> nim-regex-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> nim-kexpr-dev,</span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> nim-lapper-dev</span>
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12
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/brentp/hts-nim-tools</span>
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14
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/hts-nim-tools</span>
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<li id="1ec66a592180b9e816019238bbe6d40c69baa20e">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c#1ec66a592180b9e816019238bbe6d40c69baa20e"><strong>debian/patches/import_random.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Reinstante compatibilitz with nim 1.4</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Forward: This is effectively a backport of a change I found in the current</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> github repository. I asked to tag a new release on</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> https://github.com/brentp/hts-nim-tools/issues/11</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">Index: hts-nim-tools/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hts-nim-tools.orig/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hts-nim-tools/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -6,6 +6,7 @@</span> import lapper</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import strutils</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import tables</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> import algorithm</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import random</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import ./version</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -84,8 +85,8 @@</span> proc internal_sampler(ibam:Bam, obam:var</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"> var po = overlap_p(res[0], record)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if res[0].prob < 1 and random(1.0) < res[0].prob:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if po == 1 or po < 3.0 * random(1.0):</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if res[0].prob < 1 and rand(1.0) < res[0].prob:</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if po == 1 or po < 3.0 * rand(1.0):</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> obam.write(record)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> continue</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">import_random.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">#!/usr/bin/make -f</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">export DH_VERBOSE = 1</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">NIMCACHE=$(CURDIR)/nimcache</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">%:</span>
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5
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh $@</span>
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6
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">override_dh_auto_build:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> # needs kexpr</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> #nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/bam_filter.nim</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/hts_nim_tools.nim</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> # needs lapper</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/count_reads.nim</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/copy_number_sampler.nim</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> # works!</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim</span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim</span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr -p:/usr/share/nimble/hts src/bam_filter.nim</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim</span>
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<td class="diff-line-num new old_line" data-linenumber="16" 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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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim</span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim</span>
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<td class="diff-line-num 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">
16
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_clean:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads src/copy_number_sampler</span>
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<td class="diff-line-num new old_line" data-linenumber="19" 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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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> rm -rf $(NIMCACHE)</span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span></pre>
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