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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff">Debian Med / snpeff</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/47d6a80018c4d6d9b0250f88cd3947d947882304">47d6a800</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-22T21:25:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depending on libbiojava5-java instead of libbiojava4-java
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/17b160f68b9cbda2bc53309f017df18b610270d8">17b160f6</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-22T21:25:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/6b38b498ddc9eea5f380cb0c4d0bb79b9a801b05">6b38b498</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-22T21:27:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing d/maven.rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/3bd81514eadf7f0ecc67baef6017ea6ff83bbefa">3bd81514</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-22T22:27:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">biojava-sequencing in biojava4 is biojava-genome in biojava5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/bb6ad153c0244599e2ca1c45be161d36a06c1337">bb6ad153</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-22T22:27:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing junit4-doc as BD
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/f634677aa2982b72caca01a7cc7265c5101aa635">f634677a</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-23T21:44:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Splitting contents of patch use_... into two more precisely targetted patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/b91989116e09c62f5eae4cfbbfd8872024c0ad29">b9198911</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-23T22:32:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding forgotten import of Disabled class
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/b26f5919d0aec62a29b2c6647a33ccc470606637">b26f5919</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-02-23T22:34:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
</ul>
<h4>12 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="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#586be86c96c4f5565540f46cb13fca5585d2f3e5">
debian/libsnpeff-java.manifest
</a>
</li>
<li class="file-stats">
<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
debian/maven.rules
</a>
</li>
<li class="file-stats">
<a href="#6c594f8f0db138e4fb2dd08acce279df62b80d14">
<span class="new-file">
+
debian/patches/alternatives_to_biojava6_classes_in_biojava5.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e55e63231c28bebd84d729b0952e9a5a0f9db6d9">
<span class="deleted-file">
−
debian/patches/depending_on_biojava4.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#6849dd2847d9947187f6dfa1cf98c33b6eb2802e">
debian/patches/exclude_tests_with_missing_data.patch
</a>
</li>
<li class="file-stats">
<a href="#5978a228bf8a1ecc4b04de5fb6956877e8fb36e3">
debian/patches/omit_unused_junit_classes_and_integration_tests.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#bd2dd9ba2205aa4eef73c2ec70935b80d38a405e">
debian/patches/use_fastq_from_biojava4.patch
→
debian/patches/use_fastq_from_biojava5.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snpeff (5.1+dfsg-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Depending on libbiojava5-java instead of libbiojava4-java</span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Refreshing patches</span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Refreshing d/maven.rules</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Removing junit4-doc as build-dependency</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Putting changes related to FastQ classes and biojava5 classes into two</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> different patches</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"> -- Pierre Gruet <pgt@debian.org> Wed, 23 Feb 2022 22:32:46 +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">snpeff (5.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * New upstream version 5.1+dfsg</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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="12" 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">@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libmaven-assembly-plugin-java,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libtrove3-java,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libhtsjdk-java,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> libbiojava<span class="idiff left right">4</span>-java,</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> libbiojava<span class="idiff left right">5</span>-java,</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> junit5,</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libcommons-codec-java,</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libcommons-io-java,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,13 +21,12 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libfreemarker-java,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libjaxb-api-java,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libmaven-javadoc-plugin-java,</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> junit4-doc,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> libcommons-codec-java-doc,</span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> libcommons-io-java-doc,</span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> libcommons-math3-java-doc,</span>
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<td class="old_line diff-line-num" data-linenumber="28" 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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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> libfreemarker-java-doc,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> libhtsjdk-java-doc,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> libbiojava<span class="idiff left right">4</span>-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> libbiojava<span class="idiff left right">5</span>-java-doc,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> libtrove3-java-doc,</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> libcharts4j-java,</span>
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<td class="old_line diff-line-num" data-linenumber="33" 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="LC32" class="line" lang="plaintext"> libapfloat-java,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="41" 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">@@ -42,7 +41,7 @@ Package: libsnpeff-java</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> ${maven:Depends},</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> libbiojava<span class="idiff left right">4</span>-java,</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> libbiojava<span class="idiff left right">5</span>-java,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> libhtsjdk-java</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Suggests: ${maven:OptionalDepends},</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> libsnpeff-java-doc</span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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>
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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">@@ -18,7 +18,7 @@ Files-Excluded: */config/OLD</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> src/main/java/org/snpeff/fastq/FastqBuilder.java</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> src/main/java/org/snpeff/fastq/FastqVariant.java</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> tests/old</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Comment: The three files in src/main/java/ are provided by biojava<span class="idiff left right">4</span>-live.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Comment: The three files in src/main/java/ are provided by biojava<span class="idiff left right">5</span>-live.</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> Other files are useless or have unclear copyright.</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Files: *</span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#586be86c96c4f5565540f46cb13fca5585d2f3e5"><strong>debian/libsnpeff-java.manifest</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">/usr/share/java/snpeff.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava<span class="idiff left">4</span>-core.jar /usr/share/java/biojava<span class="idiff right">4</span>-structure.jar</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/apfloat.jar /usr/share/java/charts4j.jar /usr/share/java/commons-cli.jar /usr/share/java/trove4j.jar /usr/share/java/freemarker.jar /usr/share/java/distlib.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-math3.jar /usr/share/java/commons-io.jar /usr/share/java/commons-codec.jar /usr/share/java/biojava<span class="idiff left">5</span>-core.jar /usr/share/java/biojava<span class="idiff right">5</span>-structure.jar</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Main-Class: org.snpeff.SnpEff</span></pre>
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<li id="58530b38acb0fa3a65612c676abaea46c4a3f2f3">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#58530b38acb0fa3a65612c676abaea46c4a3f2f3"><strong>debian/maven.rules</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">junit junit jar s/4\..*/4.x/ * *</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">log4j log4j * s/1\.2\..*/1.2.x/ * *</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">net.sf.trove4j trove4j * s/.*/debian/ * *</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">org.apfloat apfloat jar s/.*/debian/ * *</span>
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<td class="old_line diff-line-num" data-linenumber="6" 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="LC4" class="line" lang="plaintext">distlib distlib jar s/.*/debian/ * *</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,4 +9,6 @@ org.freemarker freemarker jar s/.*/debian/ * *</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">org.apache.commons commons-math3 jar s/.*/debian/ * *</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">commons-io commons-io jar s/.*/debian/ * *</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">commons-codec commons-codec jar s/.*/debian/ * *</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">org.scala-lang scala-library jar s/2\..*/2.11.x/ * *</span></pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">org.biojava biojava-core jar s/.*/5.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">org.biojava biojava-genome jar s/.*/5.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">org.biojava biojava-structure jar s/.*/5.x/ * *</span></pre>
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<li id="6c594f8f0db138e4fb2dd08acce279df62b80d14">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#6c594f8f0db138e4fb2dd08acce279df62b80d14"><strong>debian/patches/alternatives_to_biojava6_classes_in_biojava5.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Modifying some calls to be compatible with biojava5-live, the</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> software being written for biojava6.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2022-02-23</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/src/main/java/org/snpeff/pdb/DistanceResult.java</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;">+++ b/src/main/java/org/snpeff/pdb/DistanceResult.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -189,19 +189,19 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> }</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"> public void setAa1(AminoAcid aa) {</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;">- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();</span></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;">+ String pdbId = aa.getChain().getParent().getPDBCode();</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> setPdbId(pdbId);</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> pdbChainId1 = aa.getChainId();</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> aaPos1 = aa.getResidueNumber().getSeqNum() - 1;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa1 = aa.getChemComp().getOneLetterCode().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa1 = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> }</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"> public void setAa2(AminoAcid aa) {</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;">- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();</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;">+ String pdbId = aa.getChain().getParent().getPDBCode();</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> setPdbId(pdbId);</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> pdbChainId2 = aa.getChainId();</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> aaPos2 = aa.getResidueNumber().getSeqNum() - 1;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa2 = aa.getChemComp().getOneLetterCode().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa2 = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> }</span>
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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"> void setPdbId(String pdbId) {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -128,7 +128,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, Chain chain, String trId, List<IdMapperEntry> idmapsOri) {</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> List<IdMapperEntry> idmapsNew = new ArrayList<>();</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> // Does chain pass filter criteria?</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> if (!filterPdbChain(chain)) return idmapsNew;</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -149,13 +149,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> int aaPos = aa.getResidueNumber().getSeqNum() - 1;</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> if (aaPos < 0) continue; // I don't know why some PDB coordinates are negative...</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char aaLetter = aa.getChemComp().getOneLetterCode().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char aaLetter = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> if (prot.length() > aaPos) {</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> char trAaLetter = prot.charAt(aaPos);</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if (aaLetter == trAaLetter) countMatch++;</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> else countMismatch++;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> } else countMismatch++;</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sb.append(aa.getChemComp().getOneLetterCode());</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;">+ sb.append(aa.getChemComp().getOne_letter_code());</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> // Only use mappings that have low error rate</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -204,7 +204,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> * transcript)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, String trId) {</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> if (debug) System.err.println("\nChecking '" + trId + "'\t<->\t'" + pdbId + "'");</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> List<IdMapperEntry> idmapsOri = idMapper.getByPdbId(pdbId);</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> List<IdMapperEntry> idmapsNew = new ArrayList<>();</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -461,7 +472,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> * Filter IdMaps for a specific chain</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> List<IdMapperEntry> idMapChain(Structure pdbStruct, Chain chain, List<IdMapperEntry> idMaps) {</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;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> List<IdMapperEntry> idMapChain = new ArrayList<>();</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> for (IdMapperEntry idmap : idMaps) {</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> if (idmap.pdbId.equals(pdbId) //</span></pre>
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<li id="e55e63231c28bebd84d729b0952e9a5a0f9db6d9">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#e55e63231c28bebd84d729b0952e9a5a0f9db6d9"><strong>debian/patches/depending_on_biojava4.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Adapt pom and imports to biojava4</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">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2022-01-23</span></span>
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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">--- a/pom.xml</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/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -101,12 +101,16 @@</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> <groupId>org.biojava</groupId></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> <artifactId>biojava-core</artifactId></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;">- <version>6.0.4</version></span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>debian</version></span></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;">+ <scope>system</scope></span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <systemPath>/usr/share/java/biojava4-core.jar</systemPath></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> <groupId>org.biojava</groupId></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> <artifactId>biojava-structure</artifactId></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>6.0.4</version></span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>debian</version></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <scope>system</scope></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;">+ <systemPath>/usr/share/java/biojava4-structure.jar</systemPath></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> <groupId>com.github.samtools</groupId></span></pre>
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<li id="6849dd2847d9947187f6dfa1cf98c33b6eb2802e">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#6849dd2847d9947187f6dfa1cf98c33b6eb2802e"><strong>debian/patches/exclude_tests_with_missing_data.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">@@ -54,3 +54,20 @@ Last-Update: 2022-01-29</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> public void test_02() {</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> Log.debug("Test");</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/testCases/unity/TestCasesNmers.java</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -1,5 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> package org.snpeff.snpEffect.testCases.unity;</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.jupiter.api.Disabled;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> import org.junit.jupiter.api.Test;</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> import org.snpeff.binseq.coder.DnaCoder;</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> import org.snpeff.nmer.Nmer;</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -47,6 +48,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> }</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>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Disabled("Needed data are not in the source tarball")</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> public void test_20_Nmers_read_write() {</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> Log.debug("Test");</span></pre>
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<li id="5978a228bf8a1ecc4b04de5fb6956877e8fb36e3">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#5978a228bf8a1ecc4b04de5fb6956877e8fb36e3"><strong>debian/patches/omit_unused_junit_classes_and_integration_tests.patch</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Last-Update: 2022-01-29</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">--- a/pom.xml</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;">+++ b/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -17<span class="idiff left">8</span>,6 +17<span class="idiff right">8</span>,9 @@</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -17<span class="idiff left">2</span>,6 +17<span class="idiff right">2</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> <encoding>ISO-8859-1</encoding></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> <showDeprecation>true</showDeprecation></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> <showWarnings>true</showWarnings></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">@@ -17,7 +17,7 @@ Last-Update: 2022-01-29</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </configuration></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">11</span>,6 +2<span class="idiff right">14</span>,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">05</span>,6 +2<span class="idiff right">08</span>,16 @@</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> <encoding>ISO-8859-1</encoding></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </configuration></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </plugin></span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">depending_on_biojava4.patch</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">alter_pom_for_debian_packaging.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">update_launching_script_and_config_file_for_Debian.patch</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">use_fastq_from_biojava<span class="idiff left right">4</span>.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">use_fastq_from_biojava<span class="idiff left right">5</span>.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">omit_unused_junit_classes_and_integration_tests.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">exclude_tests_with_missing_data.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">alternatives_to_biojava6_classes_in_biojava5.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#bd2dd9ba2205aa4eef73c2ec70935b80d38a405e"><strong>debian/patches/use_fastq_from_biojava4.patch</strong>
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<strong>debian/patches/use_fastq_from_biojava5.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Using Fastq* classes from biojava<span class="idiff left right">4</span>-live</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Using Fastq* classes from biojava<span class="idiff left right">5</span>-live</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 202<span class="idiff left">1</span>-0<span class="idiff right">3-16</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 202<span class="idiff left">2</span>-0<span class="idiff right">2-22</span></span></span>
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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">--- a/src/main/java/org/snpeff/Fastq2Fastq.java</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/main/java/org/snpeff/Fastq2Fastq.java</span></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">@@ -10,8 +10,8 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.Fastq;</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;">-import org.snpeff.fastq.FastqVariant;</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;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></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 org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</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;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></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 org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> import org.snpeff.fileIterator.FastqFileIterator;</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> import org.snpeff.util.GprSeq;</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> import org.snpeff.util.Log;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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="22" 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">@@ -22,7 +22,7 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> import java.io.InputStreamReader;</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </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;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> import org.snpeff.util.GprSeq;</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> import org.snpeff.util.Log;</span>
</pre>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,8 +34,8 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> import org.snpeff.binseq.coder.DnaQualityCoder;</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.Fastq;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> /**</span>
</pre>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> * Binary packed DNA sequence and base calling quality</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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="46" 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">@@ -46,7 +46,7 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> import java.io.IOException;</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> * DnaAndQualitySequence with an ID</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="57" 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">@@ -57,7 +57,7 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> import org.snpeff.binseq.comparator.DnaQualSubsequenceComparator;</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> import org.snpeff.binseq.comparator.DnaSubsequenceComparator;</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> import org.snpeff.util.Log;</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" 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="69" 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">@@ -69,8 +69,8 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> import org.snpeff.binseq.coder.DnaCoder;</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;">-import org.snpeff.fastq.Fastq;</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;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> import org.snpeff.fileIterator.FastqFileIterator;</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> import org.snpeff.util.Log;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" 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="82" 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">@@ -82,8 +82,8 @@ Last-Update: 2021-03-16</td>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> import org.snpeff.binseq.indexer.SuffixIndexerNmer;</span>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.Fastq;</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</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;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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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;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</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;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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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;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> import org.snpeff.fileIterator.FastaFileIterator;</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> import org.snpeff.fileIterator.FastqFileIterator;</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> import org.snpeff.util.Gpr;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="92" 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">@@ -92,7 +92,7 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"><span class="p">@@ -1,5 +1,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> package org.snpeff.fastq;</span>
</pre>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> </span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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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;">+</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"> /**</span>
</pre>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> * Simple maipulation of fastq sequences</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" 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="102" 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">@@ -102,8 +102,8 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="diff"><span class="p">@@ -1,5 +1,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"> package org.snpeff.fastq;</span>
</pre>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqBuilder;</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;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqBuilder;</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> /**</span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"> * Trim fastq sequence when quality drops below a threshold</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" 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="114" 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">@@ -114,7 +114,7 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> import java.util.Collections;</span>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> import java.util.LinkedList;</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> * Trim fastq sequence when:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" 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="125" 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">@@ -125,22 +125,20 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="diff"> import java.util.Collections;</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> import java.util.LinkedList;</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> * Trim fastq sequence when median quality drops below a threshold</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> * </span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pom.xml</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">13</span>,6 +1<span class="idiff">13</span>,1<span class="idiff right">3</span> @@</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"> <<span class="idiff left right">systemPath>/usr/share/java/biojava4-structure.jar</systemPath</span>></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left">09</span>,6 +1<span class="idiff">09</span>,1<span class="idiff right">1</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> <<span class="idiff left right">version>6.0.4</version</span>></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <groupId>org.biojava</groupId></span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>biojava4-sequencing</artifactId></span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>debian</version></span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <scope>system</scope></span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <systemPath>/usr/share/java/biojava4-sequencing.jar</systemPath></span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>biojava-genome</artifactId></span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>5.x</version></span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </dependency></span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <dependency></span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> <groupId>com.github.samtools</groupId></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">@@ -155,9 +153,9 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.Fastq;</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqBuilder;</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqBuilder;</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqBuilder;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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161
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> import org.snpeff.util.Log;</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> /**</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" 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="166" 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">@@ -168,159 +166,8 @@ Last-Update: 2021-03-16</td>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.Fastq;</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.snpeff.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">sequencing</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.Fastq;</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.biojava.nbio.<span class="idiff left right">genome</span>.io.fastq.FastqVariant;</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"> import java.io.BufferedReader;</span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="diff"> import java.io.IOException;</span></pre>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/pdb/DistanceResult.java</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/pdb/DistanceResult.java</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"><span class="p">@@ -189,19 +189,19 @@</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"> public void setAa1(AminoAcid aa) {</span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = aa.getChain().getParent().getPDBCode();</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"> setPdbId(pdbId);</span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"> pdbChainId1 = aa.getChainId();</span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> aaPos1 = aa.getResidueNumber().getSeqNum() - 1;</span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa1 = aa.getChemComp().getOneLetterCode().charAt(0);</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;">+ aa1 = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"> }</span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"> </span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"> public void setAa2(AminoAcid aa) {</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = aa.getChain().getStructure().getPDBHeader().getPdbId().toString();</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = aa.getChain().getParent().getPDBCode();</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"> setPdbId(pdbId);</span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"> pdbChainId2 = aa.getChainId();</span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"> aaPos2 = aa.getResidueNumber().getSeqNum() - 1;</span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa2 = aa.getChemComp().getOneLetterCode().charAt(0);</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa2 = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"> }</span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"> void setPdbId(String pdbId) {</span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdPdb.java</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="p">@@ -113,9 +113,9 @@</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"> Map<String, String> chain2uniproId = new HashMap<String, String>();</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"> for (DBRef dbref : pdbStruct.getDBRefs()) {</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"> if (debug)</span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Log.debug("PDB_DBREF\tchain:" + dbref.getChainName() + "\tdb: " + dbref.getDatabase() + "\tID: " + dbref.getDbAccession());</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Log.debug("PDB_DBREF\tchain:" + dbref.getChainId() + "\tdb: " + dbref.getDatabase() + "\tID: " + dbref.getDbAccession());</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"> if (dbref.getDatabase().equals(UNIPROT_DATABASE))</span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chain2uniproId.put(dbref.getChainName(), dbref.getDbAccession());</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chain2uniproId.put(dbref.getChainId(), dbref.getDbAccession());</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"> return chain2uniproId;</span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="p">@@ -128,7 +128,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"> List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, Chain chain, String trId, List<IdMapperEntry> idmapsOri) {</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"> List<IdMapperEntry> idmapsNew = new ArrayList<>();</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"> // Does chain pass filter criteria?</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"> if (!filterPdbChain(chain)) return idmapsNew;</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="p">@@ -149,13 +149,13 @@</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"> int aaPos = aa.getResidueNumber().getSeqNum() - 1;</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"> if (aaPos < 0) continue; // I don't know why some PDB coordinates are negative...</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char aaLetter = aa.getChemComp().getOneLetterCode().charAt(0);</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char aaLetter = aa.getChemComp().getOne_letter_code().charAt(0);</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"> if (prot.length() > aaPos) {</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff"> char trAaLetter = prot.charAt(aaPos);</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"> if (aaLetter == trAaLetter) countMatch++;</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"> else countMismatch++;</span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"> } else countMismatch++;</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sb.append(aa.getChemComp().getOneLetterCode());</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sb.append(aa.getChemComp().getOne_letter_code());</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"> // Only use mappings that have low error rate</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="p">@@ -171,7 +171,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"> for (IdMapperEntry idm : idmapsOri) {</span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"> if (trId.equals(idm.trId) && pdbId.equals(idm.pdbId)) {</span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- idmapsNew.add(idm.cloneAndSet(chain.getId(), pdbAaLen, trAaLen));</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ idmapsNew.add(idm.cloneAndSet(chain.getId().toString(), pdbAaLen, trAaLen));</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"><span class="p">@@ -204,7 +204,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"> * transcript)</span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"> List<IdMapperEntry> checkSequencePdbGenome(Structure pdbStruct, String trId) {</span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"> if (debug) System.err.println("\nChecking '" + trId + "'\t<->\t'" + pdbId + "'");</span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"> List<IdMapperEntry> idmapsOri = idMapper.getByPdbId(pdbId);</span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"> List<IdMapperEntry> idmapsNew = new ArrayList<>();</span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"><span class="p">@@ -300,13 +300,24 @@</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"> * Return true if the PDB's chain passes the criteria I.e.: Organism matches</span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"> boolean filterPdbChain(Chain chain) {</span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // note: Compound is replaced by EntityInfo in biojava 5.x</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (EntityInfo entityInfo : chain.getStructure().getEntityInfos()) {</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (contains(entityInfo.getOrganismCommon(), pdbOrganismCommon) || contains(entityInfo.getOrganismScientific(), pdbOrganismScientific)) {</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return true;</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return false;</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (chain.getCompound() == null) return false;</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Try 'ORGANISM_SCINETIFIC'</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String orgs = chain.getCompound().getOrganismScientific();</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (orgs != null && orgs.indexOf(pdbOrganismScientific) >= 0) return true;</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Try 'ORGANISM_COMMON'</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ orgs = chain.getCompound().getOrganismCommon();</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (orgs == null) return false;</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // Multiple organisms?</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (orgs.indexOf(' ') > 0) {</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (String org : orgs.split("\\s"))</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (org.equals(pdbOrganismCommon)) return true;</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return orgs.equals(pdbOrganismCommon);</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"><span class="p">@@ -461,7 +472,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"> * Filter IdMaps for a specific chain</span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"> List<IdMapperEntry> idMapChain(Structure pdbStruct, Chain chain, List<IdMapperEntry> idMaps) {</span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pdbId = pdbStruct.getPDBHeader().getPdbId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pdbId = pdbStruct.getPDBCode();</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff"> List<IdMapperEntry> idMapChain = new ArrayList<>();</span>
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff"> for (IdMapperEntry idmap : idMaps) {</span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"> if (idmap.pdbId.equals(pdbId) //</span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="p">@@ -523,7 +534,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"> boolean isCompound(Structure pdbStruct) {</span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- List<EntityInfo> compounds = pdbStruct.getEntityInfos();</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ List<Compound> compounds = pdbStruct.getCompounds();</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"> return compounds != null && !compounds.isEmpty();</span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="p">@@ -708,7 +719,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"> // Analyze distance between amino acids in different chains</span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff"> for (Chain chain1 : pdbStruct.getChains()) {</span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String chainId1 = chain1.getId();</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String chainId1 = chain1.getId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"> List<IdMapperEntry> idMapChain1 = idMapChain(pdbStruct, chain1, idMapConfirmed);</span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"> if (idMapChain1.isEmpty()) {</span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"> if (debug) Log.debug("Empty maps for chain '" + chainId1 + "'");</span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"><span class="p">@@ -716,7 +727,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"> for (Chain chain2 : pdbStruct.getChains()) {</span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String chainId2 = chain2.getId();</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String chainId2 = chain2.getId().toString();</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"> if (chainId1.compareTo(chainId2) >= 0) continue; // Only calculate once</span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"> // Compare UNIPROT IDs</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/snpeff/-/compare/99b80e49b0a8b7fa8a2c15627971ea3c159279ff...b26f5919d0aec62a29b2c6647a33ccc470606637#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -28,7 +28,7 @@ cp -a tests/ "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>classes/</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">javac <span class="nt" style="color: #000080;">-d</span> classes <span class="nt" style="color: #000080;">-cp</span> /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava<span class="idiff left">4</span>-core.jar:/usr/share/java/biojava<span class="idiff">4-sequencing</span>.jar:/usr/share/java/biojava<span class="idiff right">4</span>-structure.jar org/snpeff/snpEffect/testCases/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.java</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">javac <span class="nt" style="color: #000080;">-d</span> classes <span class="nt" style="color: #000080;">-cp</span> /usr/share/java/junit-jupiter-api.jar:/usr/share/java/snpeff.jar:/usr/share/java/biojava<span class="idiff left">5</span>-core.jar:/usr/share/java/biojava<span class="idiff">5-genome</span>.jar:/usr/share/java/biojava<span class="idiff right">5</span>-structure.jar org/snpeff/snpEffect/testCases/<span class="k" style="font-weight: 600;">*</span>/<span class="k" style="font-weight: 600;">*</span>.java</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Only running unit tests, not integration ones (needing data from the Internet)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell">java <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/junit-platform-console-standalone.jar <span class="nt" style="color: #000080;">--class-path</span> /usr/share/java/snpeff.jar:/usr/share/java/biojava<span class="idiff left right">4-sequencing</span>.jar:classes <span class="nt" style="color: #000080;">--select-package</span> org.snpeff.snpEffect.testCases.unity</span></pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">java <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/junit-platform-console-standalone.jar <span class="nt" style="color: #000080;">--class-path</span> /usr/share/java/snpeff.jar:/usr/share/java/biojava<span class="idiff left right">5-genome</span>.jar:classes <span class="nt" style="color: #000080;">--select-package</span> org.snpeff.snpEffect.testCases.unity</span></pre>
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