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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-eagle">Debian Med / bio-eagle</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-eagle/commit/4dcd72a70cddc0acb86255c2cdd80790b2b25fbf">4dcd72a7</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-11-24T14:00:22Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelogs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-eagle/commit/6fc119b361b7a44ed50c8194080507f1b1bc570d">6fc119b3</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-11-24T14:04:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#9c508e350e985b45f6e268390caa2ba19fb622d9">
debian/patches/Makefile_config.patch
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<li class="file-stats">
<a href="#278b1381ceeb32731ca9bdb81f1380f92a4b0b2c">
debian/upstream.changelog
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bio-eagle/compare/bae5279184f6e8e1396a24010db3a217383d2a11...6fc119b361b7a44ed50c8194080507f1b1bc570d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-eagle (2.4.1-1) 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"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Update my email address.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Dylan Aïssi <daissi@debian.org> Sat, 24 Nov 2018 14:57:37 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">bio-eagle (2.4-2) unstable; urgency=medium</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"> * Team upload</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bio-eagle/compare/bae5279184f6e8e1396a24010db3a217383d2a11...6fc119b361b7a44ed50c8194080507f1b1bc570d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: bio-eagle</span>
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<pre style="margin: 0;"> <span id="LC2" 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="LC3" class="line" lang="plaintext">Uploaders: Dylan Aïssi <<span class="idiff left right">bob.dybian@gmail.com</span>></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Dylan Aïssi <<span class="idiff left right">daissi@debian.org</span>></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11),</span>
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<li id="9c508e350e985b45f6e268390caa2ba19fb622d9">
<a href="https://salsa.debian.org/med-team/bio-eagle/compare/bae5279184f6e8e1396a24010db3a217383d2a11...6fc119b361b7a44ed50c8194080507f1b1bc570d#9c508e350e985b45f6e268390caa2ba19fb622d9"><strong>debian/patches/Makefile_config.patch</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">@@ -5,27 +5,34 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">5,14 +5,14</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">9,20 +9,20</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> ### modify these paths to local BLAS, Boost and htslib install directories</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> LBLAS = -lopenblas # alternatively -llapack (just need sgemm_)</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BLAS_DIR = /opt/openblas/0.2.14/lib</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HTSLIB_DIR = /groups/price/poru/external_software/htslib/htslib-1.4</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BLAS_DIR = /n/app/openblas/0.2.19/lib # or /n/groups/price/poru/external_software/openblas/0.2.14/lib (copied from Orchestra /opt/openblas/0.2.14/lib)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+BLAS_DIR =</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </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;">-BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install</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;">+BOOST_INSTALL_DIR =</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> # boost_1_58_0 was installed using GCC 4.8.5?</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HTSLIB_DIR = /n/groups/price/poru/external_software/htslib/htslib-1.9</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+HTSLIB_DIR =</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> ### NOTE: to reduce dependencies from htslib, configure htslib with: ./configure --disable-bz2 --disable-lzma --disable-plugins --disable-libcurl --disable-gcs --disable-s3</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> ### these paths are used only for static linking</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ZLIB_STATIC_DIR = /opt/zlib-1.2.8/lib # probably unnecessary on most systems</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> ### only for static linking (unnecessary in a local install; probably unnecessary on most systems)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ZLIB_STATIC_DIR =</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LIBSTDCXX_STATIC_DIR =</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> ### only for linking=static, which is discouraged</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ZLIB_STATIC_DIR = # probably unnecessary on most systems</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+GLIBC_STATIC_DIR =</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> ifeq ($(strip ${linking}),)</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">31,7 +3</span>1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">41,7 +4</span>1,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> LFLAGS += -pg</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> </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">@@ -34,7 +41,7 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> LFLAGS += -fopenmp</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">93,10 +93</span>,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">102,10 +102</span>,10 @@</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> .PHONY: clean</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"> $T: ${OMAIN}</span>
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<a href="https://salsa.debian.org/med-team/bio-eagle/compare/bae5279184f6e8e1396a24010db3a217383d2a11...6fc119b361b7a44ed50c8194080507f1b1bc570d#278b1381ceeb32731ca9bdb81f1380f92a4b0b2c"><strong>debian/upstream.changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/</span>
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<td class="diff-line-num old_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">
2
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<td class="diff-line-num 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">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="3" 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="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version 2.4.1 (November 18, 2018):</span>
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<td class="diff-line-num new old_line" data-linenumber="3" 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="4" 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">
4
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Allowed --noImpMissing whenever input is provided in VCF format. (Previously, --noImpMissing was only allowed in reference mode when using 1 PBWT iteration.)</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Fixed bug causing --bpStart and --bpEnd to be ignored when --chrom was not specified. (Now --chrom is required with --bpStart/--bpEnd.)</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">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Added support for multithreaded HTSlib I/O (thanks to David Heise).</span>
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<td class="diff-line-num new old_line" data-linenumber="3" 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="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Improved error-checking.</span>
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<td class="diff-line-num old_line" data-linenumber="3" 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">
3
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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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Version 2.4 (December 13, 2017):</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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">
4
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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">
9
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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="LC9" class="line" lang="plaintext"> Fixed bug that had allowed target/ref allele flips: allele-matching was only being checked when --allowRefAltSwap was specified. Also enforced requirement that --allowRefAltSwap only apply to SNPs (not indels).</span>
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<td class="diff-line-num old_line" data-linenumber="5" 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">
5
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Fixed bug causing a stack overflow for samples with very large numbers of missing genotypes (thanks to Laurent Francioli).</span>
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