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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/pbh5tools">Debian Med / pbh5tools</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/8611b48fb6cc87c7d843fc0ed4f2552885772060">8611b48f</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2015-11-15T11:02:36Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Imported Upstream version 0.8.0+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/491db2618ba0a935ee01388971fb313839a3250d">491db261</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-13T13:45:49Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.0+git20170929.58d54ff+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/d2a82d5d4210ede7280768a53810dffa1dc4b16e">d2a82d5d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:09:59Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/7385d38eff8bb426d02e5718b46004192f0fe164">7385d38e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:00Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.0+git20181212.9fa8fc4+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/8c20fd8c8323a1c48f01c755e06c228cff69b67d">8c20fd8c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:08Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.8.0+git20181212.9fa8fc4+dfsg'

Update to upstream version '0.8.0+git20181212.9fa8fc4+dfsg'

with Debian dir 23e4fc91e5a3f564af1869e80ec766531903b2f7</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/5230817223e1e6e8efb227f3b2987afa21cda3f2">52308172</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:08Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/b2dcbefe8f87f6d1c56a60f5619f8126dacf8229">b2dcbefe</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:12Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/ee109406fd70dae15bbde11cf4df1f18377105dd">ee109406</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:13Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Secure URI in copyright format

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/a73a1d9718de0e3ce17b47cf45f3a46250101e5e">a73a1d97</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:47Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: DEB_BUILD_OPTIONS allow override_dh_auto_test

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/d7fa9593dca6122a42e6b0ceec058a1afad5ccee">d7fa9593</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:47Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: Build-Depends: s/python-sphinx/python3-sphinx/

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/8519addfd2a83777c6d7030cd7836ab42a134e2a">8519addf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:10:48Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove patches enable-nosetests that are missing from debian/patches/series.

Fixes lintian: patch-file-present-but-not-mentioned-in-series

See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/0f61803d05fa18333800d6d8977b83368a746ba0">0f61803d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:29:29Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to convert from Python2 to Python3

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/dea5510302c73831ea96b8c63d2d6d97879429c0">dea55103</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:31:01Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to Uploaders

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/pbh5tools/commit/7c969ccec60aa22eb7735e988967e18e2fbc0a0a">7c969cce</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-12-07T08:34:41Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert packaging to Python3

</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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<span class="deleted-file">

−

debian/compat

</span>

</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="#555c85016bd79aa8bbb523506af81b69d9c69534">

<span class="new-file">

+

debian/patches/2to3.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#afd7845a5c185d2b4dbf7f1ce212525d02acde0c">

<span class="deleted-file">

−

debian/patches/enable-nosetests

</span>

</a>

</li>

<li class="file-stats">

<a href="#e3d6bccbde8c072befb53b9fdec6e9f77d874880">

debian/patches/multiarch-module-path.patch

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#b48a9b08d18dcde9c0f5a5bfb3eb703481306d39">

debian/python-pbh5tools.NEWS

→

debian/python3-pbh5tools.NEWS

</a>

</li>

<li class="file-stats">

<a href="#6e06d2930f2949ef6a57e07e353bdad0507e912d">

debian/python-pbh5tools.examples

→

debian/python3-pbh5tools.examples

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

doc/index.rst

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbh5tools (0.8.0+git20181212.9fa8fc4+dfsg-2) UNRELEASED; urgency=medium</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Afif Elghraoui removed himself from Uploaders</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Add myself to Uploaders</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * debhelper-compat 12</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Standards-Version: 4.4.1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  * Secure URI in copyright format</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  * Build-Depends: s/python-sphinx/python3-sphinx/</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  * Remove patches enable-nosetests that are missing from</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">    debian/patches/series.</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  * Use 2to3 to convert from Python2 to Python3</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">    Closes: #937256</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Sat, 07 Dec 2019 09:23:30 +0100</span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

</pre>

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1

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18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

</pre>

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3

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20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: pbh5tools</span>

</pre>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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3

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>

</pre>

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6

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">               dh-python,</span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">               python,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">               python-setuptools,</span>

</pre>

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9

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">               python-pbcore,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">               python-sphinx,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">               python<span class="idiff left right">-nose</span>,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">               python<span class="idiff left right">-h5py</span>,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">               python<span class="idiff left right">-cram</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">               python<span class="idiff left right">3</span>,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">               python<span class="idiff left right">3</span>-setuptools,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">               python<span class="idiff left right">3</span>-pbcore,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">               python<span class="idiff left right">3</span>-sphinx,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">               python<span class="idiff left right">3-nose <!nocheck></span>,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">               python<span class="idiff left right">3-h5py <!nocheck></span>,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">               python<span class="idiff left right">3-cram <!nocheck></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="15" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbh5tools</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbh5tools.git</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="diff-line-num new_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">

18

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/pbh5tools</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="20" 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">@@ -19,9 +20,9 @@ Homepage: https://github.com/PacificBiosciences/pbh5tools</td>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: pbh5tools</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

</td>

<td class="diff-line-num 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">

21

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

21

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<td class="diff-line-num 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">

22

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${misc:Depends},</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">         ${python:Depends},</span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">         python-pbh5tools (>= ${binary:Version}),</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">         python-pkg-resources</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">         ${python<span class="idiff left right">3</span>:Depends},</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">         python<span class="idiff left right">3</span>-pbh5tools (>= ${binary:Version}),</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext">         python<span class="idiff left right">3</span>-pkg-resources</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="plaintext">Description: tools for manipulating Pacific Biosciences HDF5 files</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext"> This package provides functionality for manipulating and extracting data</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="31" 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">@@ -30,20 +31,20 @@ Description: tools for manipulating Pacific Biosciences HDF5 files</td>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" 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"> This package is part of the SMRTAnalysis suite.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="LC33" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">Package: python-pbh5tools</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="plaintext">Package: python<span class="idiff left right">3</span>-pbh5tools</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="35" 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="LC35" class="line" lang="plaintext">Architecture: any</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" 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="LC36" class="line" lang="plaintext">Section: python</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" 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="LC37" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" 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="LC38" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">         ${python:Depends}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Description: tools for manipulating Pacific Biosciences HDF5 files -- Python <span class="idiff left right">2</span> library</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="plaintext">         ${python<span class="idiff left right">3</span>:Depends}</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Description: tools for manipulating Pacific Biosciences HDF5 files -- Python <span class="idiff left right">3</span> library</span>

</pre>

</td>

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40

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<td class="diff-line-num 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">

41

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> This package provides functionality for manipulating and extracting data</span>

</pre>

</td>

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<td class="diff-line-num old_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">

41

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<td class="diff-line-num new_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">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.</span>

</pre>

</td>

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<td class="diff-line-num 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">

42

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<td class="diff-line-num new_line" data-linenumber="43" 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">

43

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> cmp.h5 files contain alignment information while bas.h5 files contain</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="43" 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">

43

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> base-call information.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" 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">

44

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<td class="diff-line-num new_line" data-linenumber="45" 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">

45

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> pbh5tools is part of the SMRTAnalysis suite. This package provides the</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> Python <span class="idiff left right">2</span> backend library</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="47" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> Python <span class="idiff left right">3</span> backend library</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="47" 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">

47

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<td class="diff-line-num new_line" data-linenumber="48" 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">

48

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" 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="LC49" class="line" lang="plaintext">Package: python-pbh5tools-doc</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" 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">

50

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: pbh5tools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/PacificBiosciences/pbh5tools</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: doc/pacbio-theme/*</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to convert from Python2 to Python3</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/937256 </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Sat, 07 Dec 2019 09:23:30 +0100</span></span>

</pre>

</td>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</span>

</pre>

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7

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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/Makefile</span></span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -4,17 +4,17 @@</span> SHELL = /bin/bash -e</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> all: build install</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> build:</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build --executable="/usr/bin/env python"</span></span>

</pre>

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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;">+ python3 setup.py build --executable="/usr/bin/python3"</span></span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> bdist:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py build --executable="/usr/bin/env python"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py bdist --formats=egg</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py build --executable="/usr/bin/python3"</span></span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py bdist --formats=egg</span></span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> install:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py install</span></span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py install</span></span>

</pre>

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="diff"> develop:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python setup.py develop</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 setup.py develop</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> test: examples</span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">  find tests -name "*.py" | xargs nosetests -v</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/bash5tools.py</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/bash5tools.py</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</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"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> #</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -121,12 +121,12 @@</span> class BasH5ToolsRunner(PBToolRunner):</span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">         inBasH5 = BasH5Reader(self.args.inFile)</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">         if not inBasH5.hasConsensusBasecalls and self.args.readType == "ccs":</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            print "Input file %s contains no CCS reads." % self.args.inFile</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            print("Input file %s contains no CCS reads." % self.args.inFile)</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff">             sys.exit(-1)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff">         </span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">         if not inBasH5.hasRawBasecalls and self.args.readType in ["unrolled", "subreads"]:</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;">-            print "Input file %s contains no %s reads" % (self.args.inFile,</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                                          self.args.readType)</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            print("Input file %s contains no %s reads" % (self.args.inFile,</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                                          self.args.readType))</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">             sys.exit(-1)</span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff">         movieName = inBasH5.movieName</span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -145,7 +145,7 @@</span> class BasH5ToolsRunner(PBToolRunner):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">             elif inBasH5.hasConsensusBasecalls:</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">                 readType = 'ccs'</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff">             else:</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;">-                print "Input bas.h5 file has neither CCS nor subread data"</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;">+                print("Input bas.h5 file has neither CCS nor subread data")</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff">                 sys.exit(-1)</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff">         else:</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">             readType = self.args.readType</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/cmph5tools.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/cmph5tools.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

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68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> #################################################################################</span>

</pre>

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70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.</span>

</pre>

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71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> #</span>

</pre>

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72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -204,23 +204,23 @@</span> class CmpH5ToolsRunner(PBMultiToolRunner</span>

</pre>

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73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">                            outFile =  self.args.outCsv)</span>

</pre>

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74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>

</pre>

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75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">             elif cmd == 'listMetrics':</span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print '--- Metrics:'</span></span>

</pre>

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77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print "\t\n".join(DocumentedMetric.list())</span></span>

</pre>

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78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print '\n--- Statistics:'</span></span>

</pre>

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79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print "\t\n".join(DocumentedStatistic.list())</span></span>

</pre>

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80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print('--- Metrics:')</span></span>

</pre>

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81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print("\t\n".join(DocumentedMetric.list()))</span></span>

</pre>

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82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print('\n--- Statistics:')</span></span>

</pre>

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83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print("\t\n".join(DocumentedStatistic.list()))</span></span>

</pre>

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84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>

</pre>

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85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">             elif cmd == 'equal':</span>

</pre>

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86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">                 ret = cmpH5Equal(self.args.inCmp1, self.args.inCmp2)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" 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">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff">                 if not ret[0]:</span>

</pre>

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88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    print >> sys.stderr, ret[1]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="89" 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">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    print(ret[1], file=sys.stderr)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="90" 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">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff">                     return 1</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff">                 else:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="92" 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">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff">                     return 0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" 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">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="94" 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">

94

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff">             elif cmd == 'summarize':</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" 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">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff">                 for inCmp in self.args.inCmps:</span>

</pre>

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96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    print "".join(["-"] * 40)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    print cmpH5Summarize(inCmp)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    print("".join(["-"] * 40))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    print(cmpH5Summarize(inCmp))</span></span>

</pre>

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100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff">             elif cmd == 'validate':</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">                 if cmpH5Validate(self.args.inCmp):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/conf.py</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -40,8 +40,8 @@</span> source_suffix = '.rst'</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> master_doc = 'index'</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> # General information about the project.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project = u'pbh5tools'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-copyright = u'2011, devnet@pacificbiosciences.com'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project = 'pbh5tools'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" 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="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+copyright = '2011, devnet@pacificbiosciences.com'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" 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="LC115" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="116" 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="LC116" class="line" lang="diff"><span class="p">@@ -182,8 +182,8 @@</span> latex_elements = {</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" 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="LC118" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> latex_documents = [</span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  ('index', 'pbh5tools.tex', u'pbh5tools Documentation',</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-   u'devnet@pacificbiosciences.com', 'manual'),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="122" 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="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  ('index', 'pbh5tools.tex', 'pbh5tools Documentation',</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+   'devnet@pacificbiosciences.com', 'manual'),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="124" 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="LC124" class="line" lang="diff"> ]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="125" 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="LC125" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="127" 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="LC127" class="line" lang="diff"><span class="p">@@ -212,8 +212,8 @@</span> latex_documents = [</span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="128" 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="LC128" class="line" lang="diff"> # One entry per manual page. List of tuples</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" 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">

130

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> man_pages = [</span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" 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">

131

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    ('index', 'pbh5tools', u'pbh5tools Documentation',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="132" 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">

132

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-     [u'devnet@pacificbiosciences.com'], 1)</span></span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" 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">

133

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    ('index', 'pbh5tools', 'pbh5tools Documentation',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" 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">

134

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+     ['devnet@pacificbiosciences.com'], 1)</span></span>

</pre>

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</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" 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">

135

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> ]</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" 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">

136

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" 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">

137

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> # If true, show URL addresses after external links.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="138" 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">

138

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -226,7 +226,7 @@</span> man_pages = [</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="139" 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">

139

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> # (source start file, target name, title, author,</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="140" 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">

140

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> #  dir menu entry, description, category)</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> texinfo_documents = [</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  ('index', 'pbh5tools', u'pbh5tools Documentation', u'devnet@pacificbiosciences.com',</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" 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">

143

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  ('index', 'pbh5tools', 'pbh5tools Documentation', 'devnet@pacificbiosciences.com',</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff">    'pbh5tools', 'One line description of project.', 'Miscellaneous'),</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> ]</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Compare.py</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/CmpH5Compare.py</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span> import h5py as H5</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> from pbcore.io import CmpH5Reader</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="diff"> from pbh5tools.PBH5ToolsException import PBH5ToolsException</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="diff"> from pbh5tools.Metrics import *</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from mlab import rec2csv, rec2txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .mlab import rec2csv, rec2txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> def cmpH5Equal(inCmp1, inCmp2):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="diff">     """Compare two cmp.h5 files for equality. Here equality means the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span> def cmpH5Summarize(inCmp, movieSummary =</span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff">     tstr   = "filename: %s\nversion:  %s\nn reads:  %d\nn refs:   " + \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff">         "%d\nn movies: %d\nn bases:  %d\navg rl:   %d\navg acc:  %g"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff">     </span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    rl,acc,mov = zip(*[(r.readLength,r.accuracy,r.movieInfo[0]) for r in reader ])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    rl,acc,mov = list(zip(*[(r.readLength,r.accuracy,r.movieInfo[0]) for r in reader ]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff">     </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" 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="LC165" class="line" lang="diff">     summaryStr = (tstr % (os.path.basename(reader.file.filename), reader.version, len(reader),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff">                           len(reader.referenceInfoTable), len(set(mov)), NP.sum(rl),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Format.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/CmpH5Format.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="p">@@ -66,10 +66,10 @@</span> class CmpH5Format:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff">          self.STROBE_NUMBER, self.MOLECULE_ID, self.READ_START, self.READ_END,</span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff">          self.MAP_QV, self.N_MATCHES, self.N_MISMATCHES, self.N_INSERTIONS,</span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff">          self.N_DELETIONS, self.OFFSET_BEGIN, self.OFFSET_END, self.N_BACK,</span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         self.N_OVERLAP) = range(0, 22)</span></span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         self.N_OVERLAP) = list(range(0, 22))</span></span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff">         self.extraTables = ['/'.join([self.ALN_INFO, x]) for x in</span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                            cmpH5[self.ALN_INFO].keys()</span></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                            list(cmpH5[self.ALN_INFO].keys())</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff">                             if not x == self.ALN_INDEX_NAME]</span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff">         # sorting</span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff">         self.INDEX_ATTR = "Index"</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;">--- a/pbh5tools/CmpH5Merge.py</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;">+++ b/pbh5tools/CmpH5Merge.py</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="p">@@ -37,6 +37,7 @@</span> import numpy as NP</span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> from pbh5tools.PBH5ToolsException import PBH5ToolsException</span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> from pbh5tools.CmpH5Format import CmpH5Format</span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> from pbh5tools.CmpH5Utils import copyAttributes, deleteAttrIfExists</span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from functools import reduce</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> def makeRefName(rID):</span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff">     return "ref%06d" % rID</span>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="p">@@ -176,8 +177,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff">         # check for consistency of things like barcode and edna/z score</span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff">         # datasets.</span>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff">         hasBarcode = all([ fmt.BARCODE_INFO in z for z in inCmps ])</span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        extraDatasets = [set(filter(lambda x : not x == fmt.ALN_INDEX_NAME,</span></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                    z[fmt.ALN_INFO].keys())) for z in inCmps ]</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        extraDatasets = [set([x for x in list(z[fmt.ALN_INFO].keys()) if not x == fmt.ALN_INDEX_NAME]) for z in inCmps ]</span></span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff">         extraDatasets = reduce(set.intersection, extraDatasets)</span>

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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">         def filterPrint(x):</span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="p">@@ -186,7 +186,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff">                 return False</span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff">             else:</span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff">                 return True</span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        inCmps = filter(filterPrint, inCmps)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        inCmps = list(filter(filterPrint, inCmps))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff">         if not len(inCmps):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff">             raise PBH5ToolsException("merge", "No non-empty files to merge.")</span>

</pre>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="p">@@ -217,11 +217,11 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff">             # we are going to map the ref ids into the globaly unique</span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff">             # refInfoIDs.</span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            refIDMap = dict(zip(cmpH5[fmt.REF_GROUP_ID].value,</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                cmpH5[fmt.REF_GROUP_INFO_ID].value))</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            refIDMap = dict(list(zip(cmpH5[fmt.REF_GROUP_ID].value,</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                cmpH5[fmt.REF_GROUP_INFO_ID].value)))</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff">             </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;">-            refPathMap = dict(zip(cmpH5[fmt.REF_GROUP_INFO_ID].value,</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                  [os.path.basename(k) for k in cmpH5[fmt.REF_GROUP_PATH]]))</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            refPathMap = dict(list(zip(cmpH5[fmt.REF_GROUP_INFO_ID].value,</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                  [os.path.basename(k) for k in cmpH5[fmt.REF_GROUP_PATH]])))</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff">             # make a map from this cmpH5's movies to the new movie ID.</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff">             movieMap = {}</span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -233,7 +233,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff">                     raise PBH5ToolsException("merge", "Error processing movies.")</span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff">             for rID in refInfoIDs:</span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if rID not in refIDMap.values():</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                if rID not in list(refIDMap.values()):</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff">                     logging.info("Skipping reference with no reads.")</span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff">                     continue</span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff">                 if selectedReferences is not None:</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -243,7 +243,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff">                 # compute new reference ID.</span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff">                 aIdx    = cmpH5[fmt.ALN_INDEX].value</span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                refID   = {x:y for y,x in refIDMap.iteritems()}[rID]</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                refID   = {x:y for y,x in refIDMap.items()}[rID]</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff">                 refName = makeRefName(rID)</span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff">                 # which reads go to this reference.</span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="p">@@ -259,15 +259,15 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff">                 # make a map between old and new IDs</span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff">                 uAlnIDs  = NP.unique(aIdx[:,fmt.ALN_ID])</span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                alnIDMap = dict(zip(uAlnIDs, NP.array(range(0, len(uAlnIDs))) +</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                    alnIDBegin))</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                alnIDMap = dict(list(zip(uAlnIDs, NP.array(list(range(0, len(uAlnIDs)))) +</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                    alnIDBegin)))</span></span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff">                 alnGroup = {k:v for k,v in zip(cmpH5[fmt.ALN_GROUP_ID].value,</span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff">                                                cmpH5[fmt.ALN_GROUP_PATH].value) if \</span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff">                                 k in uAlnIDs}</span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff">                 newAlnGroup = [(alnIDMap[k],</span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff">                                 "/%s/%s-%d" % (refName, os.path.basename(alnGroup[k]),</span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff">                                                alnIDMap[k]),</span>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                alnGroup[k]) for k in alnGroup.keys()]</span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                alnGroup[k]) for k in list(alnGroup.keys())]</span></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">                 # Set the new ALN_ID vals in the ALN_INDEX.</span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff">                 aIdx[:,fmt.ALN_ID] = NP.array([alnIDMap[aIdx[i,fmt.ALN_ID]] for i in</span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -318,7 +318,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff">                               dtype = inCmps[0][fmt.REF_GROUP_INFO_ID].dtype)</span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff">         # reset the IDs</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;">-        outCmp[fmt.ALN_INDEX][:,fmt.ID] = range(1, outCmp[fmt.ALN_INDEX].shape[0] + 1)</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        outCmp[fmt.ALN_INDEX][:,fmt.ID] = list(range(1, outCmp[fmt.ALN_INDEX].shape[0] + 1))</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff">         # reset the molecule IDs</span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff">         outCmp[fmt.ALN_INDEX][:,fmt.MOLECULE_ID] = \</span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff">             ((NP.max(outCmp[fmt.ALN_INDEX][:,fmt.MOLECULE_ID]) *</span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -328,7 +328,7 @@</span> def cmpH5Merge(inFiles, outFile, referen</span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff">         # close the sucker.</span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff">         outCmp.close()</span>

</pre>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except Exception, e:</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;">+    except Exception as e:</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff">         try:</span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff">             # remove the file as it won't be correct</span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff">             if os.path.exists(outFile):</span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Select.py</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;">+++ b/pbh5tools/CmpH5Select.py</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="p">@@ -61,7 +61,7 @@</span> def cmpH5Select(inCmpFile, outCmp, idxs</span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff">                         where = where,</span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff">                         groupBy = groupBy,</span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff">                         groupByCsv = groupByCsv )</span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        keys = idxVecs.keys()</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        keys = list(idxVecs.keys())</span></span>

</pre>

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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">         ## XXX: Should the resultant files be sorted? </span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff">         if len(keys) == 1:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -81,7 +81,7 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff">         ids = outCmp[fmt.ALN_INDEX][:,alnIdxID]</span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff">         nds = '/'.join([groupName, idName])</span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff">         msk = NP.array([x in ids for x in inCmp[nds].value]) # got to be an NP.array</span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for dsName in inCmp[groupName].keys():</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for dsName in list(inCmp[groupName].keys()):</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff">             copyDataset('/'.join([groupName, dsName]), inCmp, outCmp,</span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff">                         msk, fmt)</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 class="p">@@ -102,12 +102,12 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff">         # copy over the AlnIndex and other AlnInfo elements</span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff">         # correpsonding to idxs to new file.</span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for dsName in inCmp[fmt.ALN_INFO].keys():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for dsName in list(inCmp[fmt.ALN_INFO].keys()):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff">             copyDataset('/'.join([fmt.ALN_INFO, dsName]), inCmp, outCmp, idxs, fmt)</span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff">         # reset the ALN_ID</span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff">         outCmp[fmt.ALN_INDEX][:,fmt.ID] = \</span>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            NP.array(range(1, outCmp[fmt.ALN_INDEX].shape[0] + 1))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            NP.array(list(range(1, outCmp[fmt.ALN_INDEX].shape[0] + 1)))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff">         # trim the other datasets</span>

</pre>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff">         trimDataset(fmt.ALN_GROUP, fmt.ALN_ID, inCmp, outCmp, fmt)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="p">@@ -115,7 +115,7 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff">         # trimDataset(fmt.MOVIE_INFO, fmt.MOVIE_ID, inCmp, outCmp, fmt)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff">         # copy Ref,Movie dataset whole</span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff">         for groupName in [fmt.REF_GROUP,fmt.MOVIE_INFO]:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            for dsName in inCmp[groupName].keys():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            for dsName in list(inCmp[groupName].keys()):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff">                 copyDataset('/'.join([groupName,dsName]), inCmp, outCmp, None, fmt)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff">         # other groups will go over whole hog</span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="p">@@ -124,7 +124,7 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff">         copyGroup(fmt.BARCODE_INFO, inCmp, outCmp)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff">         # now we copy over the actual data</span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for i in xrange(0, outCmp[fmt.ALN_GROUP_ID].shape[0]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for i in range(0, outCmp[fmt.ALN_GROUP_ID].shape[0]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff">             # figure out what reads are in this group.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff">             agID = outCmp[fmt.ALN_GROUP_ID][i]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff">             agPT = outCmp[fmt.ALN_GROUP_PATH][i]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="p">@@ -134,13 +134,13 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff">             offEnd = alnIdx[whReads, fmt.OFFSET_END]</span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff">             totalSize = NP.sum((offEnd - offBegin) + 1) # 0 in between</span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            for dsName in inCmp[agPT].keys():</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            for dsName in list(inCmp[agPT].keys()):</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff">                 fullPath = '/'.join([agPT, dsName])</span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff">                 newDs = outCmp.create_dataset(fullPath, shape = (totalSize,),</span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff">                                               dtype = inCmp[fullPath].dtype)</span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff">                 origDs = inCmp[fullPath]</span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff">                 cs = 0</span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                for j in xrange(0, len(whReads)):</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                for j in range(0, len(whReads)):</span></span>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff">                     newEnd = cs + offEnd[j] - offBegin[j]</span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff">                     newDs[cs:newEnd] = origDs[offBegin[j]:offEnd[j]]</span>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff">                     outCmp[fmt.ALN_INDEX][whReads[j],fmt.OFFSET_BEGIN] = cs</span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="p">@@ -158,7 +158,7 @@</span> def doSelect(inCmpFile, outCmpFile, idxs</span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff">         logging.debug("Closing output cmp.h5 file.")</span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff">         outCmp.close()</span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except Exception, e:</span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except Exception as e:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff">         logging.exception(e)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff">         try:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff">             os.remove(outCmpFile)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Sort.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/CmpH5Sort.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="p">@@ -42,6 +42,7 @@</span> from pbh5tools.PBH5ToolsException import</span>

</pre>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> from pbh5tools.CmpH5Format import CmpH5Format</span>

</pre>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> import pbcore.io.rangeQueries as RQ</span>

</pre>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from functools import reduce</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> def numberWithinRange(s, e, vec):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff">     """</span>

</pre>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="p">@@ -51,7 +52,7 @@</span> def numberWithinRange(s, e, vec):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff">     """</span>

</pre>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff">     lI = RQ.leftmostBinSearch(vec, s)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff">     rI = RQ.rightmostBinSearch(vec, e)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return(len(filter(lambda x : s <= x < e, vec[lI:rI])))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return(len([x for x in vec[lI:rI] if s <= x < e]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> </span>

</pre>

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377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="378" 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">

378

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> def computeIndices(tStart, tEnd):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="379" 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">

379

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="p">@@ -145,7 +146,7 @@</span> def __pathExists(h5, path):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="380" 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">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff">     try:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="381" 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">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff">         h5[path]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="382" 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">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff">         return True</span>

</pre>

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383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except Exception, E:</span></span>

</pre>

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384

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except Exception as E:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="385" 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">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff">         return False</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="386" 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="LC386" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="387" 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="LC387" class="line" lang="diff"> def __repackDataArrays(cH5, format, fixedMem = False, maxDatasetSize = 2**31 - 1):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="388" 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="LC388" class="line" lang="diff"><span class="p">@@ -153,7 +154,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="389" 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="LC389" class="line" lang="diff">     Flatten read groups according to an indexed cmp.h5 file.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff">     """</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="391" 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="LC391" class="line" lang="diff">     alnGroups = [x for x in cH5[format.ALN_GROUP_PATH]]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="392" 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="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    pulseDatasets = [cH5[x].keys() for x in alnGroups]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="393" 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="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    pulseDatasets = [list(cH5[x].keys()) for x in alnGroups]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="394" 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">

394

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff">     uPulseDatasets = sorted(list(reduce(lambda x,y: set.union(set(x), set(y)), pulseDatasets)))</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="395" 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">

395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="396" 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">

396

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff">     # check to make sure that all aln groups have the same datasets -</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="397" 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">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="p">@@ -170,13 +171,13 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff">               raise PBH5ToolsException("sort", "Datasets must agree:\n" + ",".join(spd) +</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="399" 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="LC399" class="line" lang="diff">                                        "\nvs\n" + ",".join(uPulseDatasets))</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="400" 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="LC400" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="401" 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="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    readGroupPaths = dict(zip(cH5[format.ALN_GROUP_ID],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="402" 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">

402

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                              [x for x in cH5[format.ALN_GROUP_PATH]]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="403" 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">

403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    refGroupPaths  = dict(zip(cH5[format.REF_GROUP_ID],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="404" 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">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                              [x for x in cH5[format.REF_GROUP_PATH]]))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="405" 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">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    uPDAndType     = dict(zip(uPulseDatasets,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" 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">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                              [cH5[readGroupPaths.values()[0]][z].dtype</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" 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">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                               for z in uPulseDatasets]))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="408" 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">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    readGroupPaths = dict(list(zip(cH5[format.ALN_GROUP_ID],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="409" 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">

409

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                              [x for x in cH5[format.ALN_GROUP_PATH]])))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" 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="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    refGroupPaths  = dict(list(zip(cH5[format.REF_GROUP_ID],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="411" 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">

411

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                              [x for x in cH5[format.REF_GROUP_PATH]])))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="412" 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">

412

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    uPDAndType     = dict(list(zip(uPulseDatasets,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="413" 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="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                              [cH5[list(readGroupPaths.values())[0]][z].dtype</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="414" 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="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                               for z in uPulseDatasets])))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="415" 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="LC415" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" 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="LC416" class="line" lang="diff">     ## XXX : this needs to be augmented with some saftey on not</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" 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">

417

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff">     ## loading too much data.  - set a bound on the number of elts in</span>

</pre>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="p">@@ -185,7 +186,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff">     def getData(read, ds, start, end):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff">         key = "/".join((readGroupPaths[read[format.ALN_ID]], ds))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if not pdsCache.has_key(key):</span></span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if key not in pdsCache:</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff">             logging.debug("Cacheing: %s" % key)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff">             h5DS = cH5[key]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff">             smallEnoughToFitInMemory = ((h5DS.len() * h5DS.dtype.itemsize)/1024**3) < 12</span>

</pre>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="p">@@ -200,7 +201,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff">     def chooseAlnGroupNames(gID, readBlocks, start = 1):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff">          rGroup = cH5[refGroupPaths[gID]]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         currentGroups = rGroup.keys()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         currentGroups = list(rGroup.keys())</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff">          pref = 'rg' + str(start) + '-'</span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff">          newNames = [ pref + str(i) for i,j in enumerate(readBlocks) ]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff">          if any([ nn in currentGroups for nn in newNames ]):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="p">@@ -217,7 +218,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff">     currentAlnID = 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff">     refGroupAlnGroups = []</span>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for row in xrange(0, offsets.shape[0]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for row in range(0, offsets.shape[0]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff">         logging.info("Processing reference: %d of %d" %</span>

</pre>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff">                      (row + 1, offsets.shape[0]))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="p">@@ -235,7 +236,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff">         readBlocks = []</span>

</pre>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff">         if tSize >= maxDatasetSize:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff">              lastStart  = 0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-             for i in xrange(0, len(clens)):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+             for i in range(0, len(clens)):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff">                   if clens[i]-clens[lastStart] >= maxDatasetSize:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff">                        readBlocks.append((lastStart, i))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff">                        lastStart = i</span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="p">@@ -259,7 +260,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff">                   newDS = NP.zeros(dsLength, dtype = uPDAndType[pulseDataset])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff">                   currentStart = 0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                  for readIdx in xrange(readBlock[0], readBlock[1]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                  for readIdx in range(readBlock[0], readBlock[1]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff">                        read = reads[readIdx, ]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff">                        gStart, gEnd = currentStart, currentStart + alens[readIdx]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff">                        newDS[gStart:gEnd] = getData(read, pulseDataset,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="p">@@ -271,7 +272,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff">                   newGroup.create_dataset(pulseDataset, data = newDS,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff">                                           dtype = uPDAndType[pulseDataset],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff">                                           maxshape = (None, ), chunks = (16384,))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                  logging.debug("flushing:" + ",".join(pdsCache.keys()))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                  logging.debug("flushing:" + ",".join(list(pdsCache.keys())))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff">                   pdsCache = {}</span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="p">@@ -279,7 +280,7 @@</span> def __repackDataArrays(cH5, format, fixe</span>

</pre>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff">              ## once you have moved all data for a readBlock you can change</span>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff">              ## the offsets.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff">              currentStart = 0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-             for readIdx in xrange(readBlock[0], readBlock[1]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+             for readIdx in range(readBlock[0], readBlock[1]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff">                   read = reads[readIdx, ]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff">                   gStart, gEnd = currentStart, currentStart + alens[readIdx]</span>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff">                   reads[readIdx, format.OFFSET_BEGIN] = gStart</span>

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="p">@@ -299,21 +300,21 @@</span> def __repackDataArrays(cH5, format, fixe</span>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff">              refGroupAlnGroups.append("/".join((refGroupPaths[groupID], ngn)))</span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff">     ## re-identify them.</span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    sAI[:,format.ID] = range(1, sAI.shape[0] + 1)</span></span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    sAI[:,format.ID] = list(range(1, sAI.shape[0] + 1))</span></span>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff">     assert(len(refGroupAlnGroups) == currentAlnID - 1)</span>

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff">     logging.info("Writing new AlnGroupPath values.")</span>

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff">     del(cH5[format.ALN_GROUP_PATH])</span>

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff">     del(cH5[format.ALN_GROUP_ID])</span>

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    cH5.create_dataset(format.ALN_GROUP_PATH, data = map(str, refGroupAlnGroups),</span></span>

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    cH5.create_dataset(format.ALN_GROUP_PATH, data = list(map(str, refGroupAlnGroups)),</span></span>

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff">                        ## XXX : unicode.</span>

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff">                        dtype = H5.special_dtype(vlen = str), maxshape = (None,),</span>

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff">                        chunks = (256,))</span>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    cH5.create_dataset(format.ALN_GROUP_ID, data = range(1, currentAlnID),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    cH5.create_dataset(format.ALN_GROUP_ID, data = list(range(1, currentAlnID)),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff">                        dtype = "int32", maxshape = (None,), chunks = (256,))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff">     logging.info("Wrote new AlnGroupPath values.")</span>

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for rg in readGroupPaths.values():</span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for rg in list(readGroupPaths.values()):</span></span>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff">          ## this should never be false, however, MC has produced</span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff">          ## files in the past where there are duplicate paths with</span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff">          ## different IDs and therefore you'll error here (probably</span>

</pre>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="p">@@ -379,7 +380,7 @@</span> def cmpH5Sort(inFile, outFile, tmpDir, d</span>

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff">         logging.info("Read cmp.h5 with version %s" % format.VERSION)</span>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff">         aI = cH5[format.ALN_INDEX]</span>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        originalAttrs = aI.attrs.items()</span></span>

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        originalAttrs = list(aI.attrs.items())</span></span>

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff">         ## empty is a special case. In general, h5py handles</span>

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff">         ## zero-length slices poorly and therefore I don't want to</span>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="p">@@ -396,8 +397,8 @@</span> def cmpH5Sort(inFile, outFile, tmpDir, d</span>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff">         # scope of a cmp.h5 file. We need to map format.REF_ID to its</span>

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff">         # REF_INFO_ID which is stable over merge/sort/split</span>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff">         # operations.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        refIdToInfoId = dict(zip(cH5[format.REF_GROUP_ID].value,</span></span>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                 cH5[format.REF_GROUP_INFO_ID]))</span></span>

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        refIdToInfoId = dict(list(zip(cH5[format.REF_GROUP_ID].value,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                                 cH5[format.REF_GROUP_INFO_ID])))</span></span>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff">         refInfoIds = NP.array([refIdToInfoId[i] for i in aI[:,format.REF_ID]])</span>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff">         aord = NP.lexsort([aI[:,format.TARGET_END], aI[:,format.TARGET_START],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff">                            refInfoIds])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="p">@@ -482,7 +483,7 @@</span> def cmpH5Sort(inFile, outFile, tmpDir, d</span>

</pre>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff">                                    maxshape = tuple([None for x in eTable.shape]))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff">                 logging.info("Sorted dataset: %s" % extraTable)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff">                 logging.info("Writing attributes")</span>

</pre>

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                for k in originalAttrs.keys():</span></span>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                for k in list(originalAttrs.keys()):</span></span>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff">                      # this block is necessary because I need to</span>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff">                      # convert the dataset into a string dataset from</span>

</pre>

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff">                      # object because an apparent h5py limitation.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="p">@@ -499,7 +500,7 @@</span> def cmpH5Sort(inFile, outFile, tmpDir, d</span>

</pre>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff">         ## set this flag for before.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff">         success = True</span>

</pre>

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except Exception, E:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except Exception as E:</span></span>

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff">          logging.error(E)</span>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff">          logging.exception(E)</span>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Stats.py</span></span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/CmpH5Stats.py</span></span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="p">@@ -31,11 +31,11 @@</span></span>

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> import numpy as NP</span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> import sys</span>

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from mlab import rec2csv, rec2txt</span></span>

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .mlab import rec2csv, rec2txt</span></span>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"> from pbh5tools.Metrics import *</span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> def prettyPrint(res):</span>

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print rec2txt(res, padding = 20, precision = 2)</span></span>

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(rec2txt(res, padding = 20, precision = 2))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> def makeTblFromInput(exprStr, defaultValue):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff">     if not exprStr:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/CmpH5Utils.py</span></span>

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/CmpH5Utils.py</span></span>

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="p">@@ -47,10 +47,10 @@</span> def deleteIfExists(ds, nm):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff">         del ds[nm]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> def copyAttributes(inDs, outDs):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for k in inDs.attrs.keys():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for k in list(inDs.attrs.keys()):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff">         logging.debug("copying attribute: %s" % k)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff">         elt = inDs.attrs[k]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if isinstance(elt, basestring):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if isinstance(elt, str):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff">             # h5py wants to simplify things down, so I think that this</span>

</pre>

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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff">             # is a possibility.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff">             # preserve numpy string type if possible</span>

</pre>

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/Metrics.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/Metrics.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="p">@@ -144,7 +144,7 @@</span> def processClass(cls, name, bases, dct):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff">     ignoreRes = ['^Default', '^Metric$', '^Statistic$', '^Factor$',</span>

</pre>

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff">                  '^FactorStatistic']</span>

</pre>

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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if not any(map(lambda x : re.match(x, name), ignoreRes)):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if not any([re.match(x, name) for x in ignoreRes]):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff">         if '__init__' in dct:</span>

</pre>

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585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff">             # if it has an init it takes arguments which define the</span>

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff">             # metric.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="p">@@ -179,7 +179,7 @@</span> class DocumentedMetric(type):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff">     @staticmethod</span>

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff">     def list():</span>

</pre>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return filter(lambda x : x, DocumentedMetric.Metrics)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return [x for x in DocumentedMetric.Metrics if x]</span></span>

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> class DocumentedStatistic(type):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff">     Statistics = []</span>

</pre>

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="p">@@ -190,10 +190,9 @@</span> class DocumentedStatistic(type):</span>

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff">     @staticmethod</span>

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff">     def list():</span>

</pre>

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return filter(lambda x : x, DocumentedStatistic.Statistics)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return [x for x in DocumentedStatistic.Statistics if x]</span></span>

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class Statistic(Expr):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __metaclass__ = DocumentedStatistic</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class Statistic(Expr, metaclass=DocumentedStatistic):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff">     def __init__(self, metric):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff">         self.metric = metric</span>

</pre>

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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="p">@@ -208,9 +207,7 @@</span> class Statistic(Expr):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff">     def __str__(self):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff">         return self.__class__.__name__ + '(' + str(self.metric) + ')'</span>

</pre>

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class Metric(Expr):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __metaclass__ = DocumentedMetric</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class Metric(Expr, metaclass=DocumentedMetric):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff">     def eval(self, cmpH5, idx):</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="618" 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="LC618" class="line" lang="diff">         return self.produce(cmpH5, idx)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="p">@@ -232,7 +229,7 @@</span> class Tbl(object):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff">         for a in self.cols:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff">             yield (a, self.cols[a])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff">     def eval(self, cmpH5, idx):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return [(a, self.cols[a].eval(cmpH5, idx)) for a in self.cols.keys()]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return [(a, self.cols[a].eval(cmpH5, idx)) for a in list(self.cols.keys())]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"> def split(x, f):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff">     # I'm thinking it is faster to do the allocation of the NP array</span>

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="p">@@ -240,15 +237,15 @@</span> def split(x, f):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff">     assert(len(x) == len(f))</span>

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff">     levels  = NP.unique(f)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff">     counts  = {k:0 for k in levels}</span>

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(0, len(x)):</span></span>

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(0, len(x)):</span></span>

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff">         counts[f[i]] += 1</span>

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    results = { k:NP.zeros(v, dtype = int) for k,v in counts.items() }</span></span>

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(0, len(x)):</span></span>

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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    results = { k:NP.zeros(v, dtype = int) for k,v in list(counts.items()) }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(0, len(x)):</span></span>

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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff">         k = f[i]</span>

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff">         results[k][counts[k] - 1] = x[i]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff">         counts[k] -= 1</span>

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff">     # reverse it.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return { k:v[::-1] for k,v in results.items() }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return { k:v[::-1] for k,v in list(results.items()) }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> def toRecArray(res):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="p">@@ -349,9 +346,7 @@</span> class Round(Statistic):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> ## Additionally, FactorStatistics can be computed using a group by -</span>

</pre>

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> ## it is only the case that you need this in a where where you need</span>

</pre>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> ## this new concept.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class ByFactor(Metric):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __metaclass__ = DocumentedMetric</span></span>

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<pre style="margin: 0;">+<span id="LC655" 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="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class ByFactor(Metric, metaclass=DocumentedMetric):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff">     def __init__(self, metric, factor, statistic):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff">         self.metric     = metric</span>

</pre>

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff">         self.factor     = factor</span>

</pre>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="p">@@ -359,9 +354,9 @@</span> class ByFactor(Metric):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff">     def produce(self, cmpH5, idx):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff">         r   = self.metric.eval(cmpH5, idx)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        fr  = split(range(len(idx)), self.factor.eval(cmpH5, idx))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        fr  = split(list(range(len(idx))), self.factor.eval(cmpH5, idx))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff">         res = NP.zeros(len(idx), dtype = NP.int)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for v in fr.values():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for v in list(fr.values()):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff">             res[v] = self.statistic.f(r[v])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff">         return res</span>

</pre>

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="p">@@ -468,8 +463,8 @@</span> class _MoleculeId(Factor):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> class _MoleculeName(Factor):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff">     def produce(self, cmpH5, idx):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        molecules = zip(cmpH5.alignmentIndex['MovieID'][idx],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        cmpH5.alignmentIndex['HoleNumber'][idx])</span></span>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        molecules = list(zip(cmpH5.alignmentIndex['MovieID'][idx],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        cmpH5.alignmentIndex['HoleNumber'][idx]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff">         return NP.array(['%s_%s' % (m,h) for m,h in molecules])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> class _Strand(Factor):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="p">@@ -553,15 +548,15 @@</span> DefaultSortBy       = Tbl(alignmentIdx =</span>

</pre>

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> def query(reader, what = DefaultWhat, where = DefaultWhere,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff">           groupBy = DefaultGroupBy, groupByCsv = None, </span>

</pre>

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff">           sortBy = DefaultSortBy, limit = None):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    idxs = NP.where(where.eval(reader, range(0, len(reader))))[0]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    idxs = NP.where(where.eval(reader, list(range(0, len(reader)))))[0]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff">     if groupByCsv:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff">         groupBy = groupCsv(groupByCsv, idxs, reader)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff">     else:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff">         groupBy = groupBy.eval(reader, idxs)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff">     results = {}</span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff">     </span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for k,v in split(idxs, groupBy).items():</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for k,v in list(split(idxs, groupBy).items()):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff">         sortVals = sortBy.eval(reader, v)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        sortIdxs = v[NP.lexsort(map(lambda z : z[1], sortVals)[::-1])][:limit]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        sortIdxs = v[NP.lexsort([z[1] for z in sortVals][::-1])][:limit]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff">         results[k] = what.eval(reader, sortIdxs)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff">     return results</span>

</pre>

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/cbook.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/cbook.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span> from the Python Cookbook -- hence the na</span>

</pre>

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> """</span>

</pre>

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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> def is_string_like(obj):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff">     'Return True if *obj* looks like a string'</span>

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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if isinstance(obj, (str, unicode)):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if isinstance(obj, str):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff">         return True</span>

</pre>

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff">     # numpy strings are subclass of str, ma strings are not</span>

</pre>

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff">     if ma.isMaskedArray(obj):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pbh5tools/mlab.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pbh5tools/mlab.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="p">@@ -47,7 +47,7 @@</span> A collection of helper methods for numpy</span>

</pre>

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> """</span>

</pre>

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> </span>

</pre>

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718

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> import csv, os, copy</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="719" 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">

719

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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cbook</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import cbook</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> import numpy as np</span>

</pre>

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722

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> </span>

</pre>

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723

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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> # a series of classes for describing the format intentions of various rec views</span>

</pre>

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724

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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="p">@@ -320,7 +320,7 @@</span> def rec2txt(r, header=None, padding=3, p</span>

</pre>

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725

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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff">        </span>

</pre>

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726

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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> </span>

</pre>

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727

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff">         if ntype==np.int or ntype==np.int16 or ntype==np.int32 or ntype==np.int64 or ntype==np.int8 or ntype==np.int_:</span>

</pre>

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728

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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            length = max(len(colname),np.max(map(len,map(str,column))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="729" 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">

729

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            length = max(len(colname),np.max(list(map(len,list(map(str,column))))))</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="730" 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">

730

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff">             return 1, length+padding, "%d" # right justify</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="731" 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">

731

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="732" 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">

732

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff">         # JDH: my powerbook does not have np.float96 using np 1.3.0</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="733" 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">

733

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="p">@@ -337,7 +337,7 @@</span> def rec2txt(r, header=None, padding=3, p</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="734" 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">

734

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff">         """</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="735" 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">

735

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff">         if ntype==np.float or ntype==np.float32 or ntype==np.float64 or (hasattr(np, 'float96') and (ntype==np.float96)) or ntype==np.float_:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="736" 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">

736

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff">             fmt = "%." + str(precision) + "f"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="737" 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">

737

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            length = max(len(colname),np.max(map(len,map(lambda x:fmt%x,column))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="738" 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">

738

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            length = max(len(colname),np.max(list(map(len,[fmt%x for x in column]))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="739" 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">

739

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff">             return 1, length+padding, fmt   # right justify</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="740" 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">

740

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="741" 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">

741

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="742" 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">

742

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"><span class="p">@@ -345,7 +345,7 @@</span> def rec2txt(r, header=None, padding=3, p</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="743" 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">

743

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff">             length = max(len(colname),column.itemsize)</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="744" 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">

744

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff">             return 1, length+padding, "%s" # left justify // JHB changed the 0 to a 1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" 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">

745

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="746" 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">

746

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        return 0, max(len(colname),np.max(map(len,map(str,column))))+padding, "%s"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="747" 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">

747

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        return 0, max(len(colname),np.max(list(map(len,list(map(str,column))))))+padding, "%s"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="748" 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">

748

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="749" 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">

749

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff">     if header is None:</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" 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">

750

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff">         header = r.dtype.names</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="751" 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">

751

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/bash5tools.t</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="752" 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">

752

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/bash5tools.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="753" 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">

753

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="p">@@ -3,8 +3,8 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="754" 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">

754

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> </span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="755" 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">

755

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"> Set up some vars ...</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="756" 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">

756

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="757" 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">

757

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ INH5=`python -c "from pbcore import data; print data.getBasH5s()[0]"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="758" 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">

758

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ MOVIENAME=$(basename `python -c "from pbcore import data; print data.getBasH5s()[0][:-7]"`)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="759" 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">

759

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ INH5=`python3 -c "from pbcore import data; print(data.getBasH5s()[0])"`</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="760" 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">

760

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ MOVIENAME=$(basename `python3 -c "from pbcore import data; print(data.getBasH5s()[0][:-7])"`)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="761" 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">

761

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff">   $ CMD="bash5tools.py $INH5"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="762" 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">

762

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="763" 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">

763

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff">   $ $CMD --readType=ccs</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="764" 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">

764

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/merge.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="765" 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">

765

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/merge.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" 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">

766

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="767" 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">

767

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" 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">

768

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ export INH5=`python3 -c "from pbcore import data ; print(data.getCmpH5())"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="769" 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">

769

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff">   $ cmph5tools.py select $INH5 --outFile left.cmp.h5 --idx 0 1 2 3</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="770" 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">

770

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff">   $ echo $?  </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="771" 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">

771

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff">   0</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="772" 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">

772

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/select.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="773" 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">

773

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/select.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="774" 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">

774

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="775" 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">

775

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff">   $ . $TESTDIR/portability.sh</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="776" 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">

776

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="777" 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">

777

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> Set up basic commands</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="778" 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">

778

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="779" 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">

779

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ INH5=`python3 -c "from pbcore import data ; print(data.getCmpH5())"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="780" 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">

780

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff">   $ CMD="cmph5tools.py stats $INH5"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="781" 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">

781

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> Test basic output</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="782" 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">

782

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff">   $ $CMD --what "ReadStart" --limit 5</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="783" 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">

783

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/sort.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="784" 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">

784

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/sort.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="785" 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">

785

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="786" 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">

786

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="787" 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">

787

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ export INH5=`python3 -c "from pbcore import data ; print(data.getCmpH5())"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="788" 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">

788

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff">   $ cmph5tools.py sort --deep --outFile tmp.cmp.h5 $INH5</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="789" 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">

789

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff">   $ echo $?  </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="790" 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">

790

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff">   0</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="791" 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">

791

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="792" 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">

792

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff">   $ cmph5tools.py sort --outFile ftmp.cmp.h5 $INH5</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="793" 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">

793

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff">   $ echo $?</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="794" 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">

794

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff">   0</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="795" 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">

795

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ python -c "from pbcore.io import CmpH5Reader; a = CmpH5Reader('tmp.cmp.h5'); b = CmpH5Reader('ftmp.cmp.h5'); print(all([a[i] == b[i] for i in xrange(len(a))]));"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="796" 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">

796

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ python3 -c "from pbcore.io import CmpH5Reader; a = CmpH5Reader('tmp.cmp.h5'); b = CmpH5Reader('ftmp.cmp.h5'); print(all([a[i] == b[i] for i in xrange(len(a))]));"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="797" 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">

797

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff">   True</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="798" 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">

798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff">   $ cmph5tools.py sort --outFile ptmp.cmp.h5 --deep --usePythonIndexer $INH5</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="799" 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">

799

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff">   $ echo $?</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="800" 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">

800

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/stats.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="801" 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">

801

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/stats.t</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="802" 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">

802

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="803" 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">

803

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff">   $ . $TESTDIR/portability.sh</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="804" 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">

804

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="805" 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">

805

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> Set up inputs and basic command string.</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="806" 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">

806

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="807" 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">

807

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ INH5=`python3 -c "from pbcore import data ; print(data.getCmpH5())"`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="808" 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">

808

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff">   $ CMD="cmph5tools.py stats $INH5"</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="809" 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">

809

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="810" 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">

810

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> Print Readlength to stdout</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="811" 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">

811

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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/cram/valid.t</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="812" 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">

812

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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/cram/valid.t</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="813" 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">

813

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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="p">@@ -1,2 +1,2 @@</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="814" 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">

814

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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="815" 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">

815

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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $ export INH5=`python3 -c "from pbcore import data ; print(data.getCmpH5())"`</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="816" 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">

816

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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff">   $ cmph5tools.py validate $INH5</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="817" 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">

817

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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_cmph5lib_CmpH5Sort.py</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="818" 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">

818

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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_cmph5lib_CmpH5Sort.py</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="819" 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">

819

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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="p">@@ -11,19 +11,19 @@</span> import pbcore.io.rangeQueries as RQ</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="820" 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">

820

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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> from pbcore.io import CmpH5Reader</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="821" 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">

821

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="822" 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">

822

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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> def brute_force_number_in_range(s, e, vec):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="823" 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">

823

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return(len(filter(lambda x : s <= x < e, vec)))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="824" 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">

824

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return(len([x for x in vec if s <= x < e]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="825" 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">

825

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="826" 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">

826

</td>

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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"> def generate_positions(size, coverage, lScale = 50):</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="827" 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">

827

</td>

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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff">     NN = int(size*coverage)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="828" 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">

828

</td>

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff">     tS = random.randint(0, size, NN)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="829" 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">

829

</td>

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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    tE = tS + array(map(int, random.exponential(lScale, NN) + 1))</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="830" 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">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    tE = tS + array(list(map(int, random.exponential(lScale, NN) + 1)))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="831" 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">

831

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff">     ar = array([tS, tE]).transpose()</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="832" 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">

832

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff">     ar = ar[lexsort((tE, tS)),]</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="833" 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">

833

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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff">     return(ar)</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="834" 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">

834

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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="835" 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">

835

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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"> def brute_force_search(tStart, tEnd, nBack, nOverlap, start, end):</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="836" 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">

836

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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff">     toKeep = array([False]*len(tStart))</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="837" 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">

837

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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    res = array(range(0, len(tStart)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="838" 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">

838

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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    res = array(list(range(0, len(tStart))))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="839" 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">

839

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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="840" 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">

840

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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff">     for i in range(0, len(tStart)):</span>

</pre>

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841

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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff">         # four cases to deal with.</span></pre>

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<br>

</li>

<li id="afd7845a5c185d2b4dbf7f1ce212525d02acde0c">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#afd7845a5c185d2b4dbf7f1ce212525d02acde0c"><strong>debian/patches/enable-nosetests</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Configure nosetests to run with setup.py test</span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Afif Elghraoui <afif@ghraoui.name></span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2015-08-12</span></span>

</pre>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pbh5tools.orig/setup.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pbh5tools/setup.py</span></span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -26,6 +26,7 @@</span></span>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">                'bin/cmph5tools.py'],</span>

</pre>

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9

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">     packages = find_packages("."),</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">     package_dir = {'':'.'},</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test_suite = 'nose.collector',</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">     ext_modules=[Extension('pbh5tools/ci', ['pbh5tools/ci.c'],</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">                            extra_compile_args=["-O3","-shared"])],</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">     zip_safe = False,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pbh5tools/setup.cfg</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -0,0 +1,3 @@</span></span>

</pre>

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18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+[nosetests]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+verbosity=2</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+where=tests</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="e3d6bccbde8c072befb53b9fdec6e9f77d874880">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#e3d6bccbde8c072befb53b9fdec6e9f77d874880"><strong>debian/patches/multiarch-module-path.patch</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,9 @@ Author: Afif Elghraoui</td>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2016-03-20 00:45:22 -0700</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Enable multiarch modules</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">python-pbh5tools.orig</span>/pbh5tools/Indexer.py</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">python-pbh5tools</span>/pbh5tools/Indexer.py</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,10 +32,11 @@</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/pbh5tools/Indexer.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/pbh5tools/Indexer.py</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -32,10 +32,11 @@</span><span class="idiff left right"> import ctypes</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> import os</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> import numpy</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> import pkg_resources</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,3 +6,4 @@ ignore-cram-results.patch</td>

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<td class="diff-line-num old_line" 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">

6

</td>

<td class="diff-line-num new_line" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">fix-type-in-test.patch</span>

</pre>

</td>

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<td class="diff-line-num old_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">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">multiarch-module-path.patch</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># enable-nosetests</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">2to3.patch</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b48a9b08d18dcde9c0f5a5bfb3eb703481306d39">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#b48a9b08d18dcde9c0f5a5bfb3eb703481306d39"><strong>debian/python-pbh5tools.NEWS</strong>

→

<strong>debian/python3-pbh5tools.NEWS</strong>

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

</table>

<br>

</li>

<li id="6e06d2930f2949ef6a57e07e353bdad0507e912d">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#6e06d2930f2949ef6a57e07e353bdad0507e912d"><strong>debian/python-pbh5tools.examples</strong>

→

<strong>debian/python3-pbh5tools.examples</strong>

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ BINDIR=$(CURDIR)/debian/pbh5tools/usr/bin</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_NAME = pbh5tools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">     LC_ALL=C.UTF-8 dh $@ --with python<span class="idiff left right">2</span> --buildsystem=pybuild</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     LC_ALL=C.UTF-8 dh $@ --with python<span class="idiff left right">3</span> --buildsystem=pybuild</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

12

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<td class="diff-line-num 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">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_build:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">     dh_auto_build</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,13 +19,15 @@ override_dh_install:</td>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

19

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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext">     # We do this here rather than in .install files so that debhelper</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext">     # takes care of the #!/usr/bin/env lines for us</span>

</pre>

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<td class="diff-line-num 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">

21

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">     mkdir -p $(BINDIR)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">     mv debian/python-pbh5tools/usr/bin/bash5tools.py $(BINDIR)/bash5tools</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">     mv debian/python-pbh5tools/usr/bin/cmph5tools.py $(BINDIR)/cmph5tools</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="24" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext">     mv debian/python<span class="idiff left right">3</span>-pbh5tools/usr/bin/bash5tools.py $(BINDIR)/bash5tools</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">     mv debian/python<span class="idiff left right">3</span>-pbh5tools/usr/bin/cmph5tools.py $(BINDIR)/cmph5tools</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" 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">

24

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<td class="diff-line-num new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext">override_dh_auto_test:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="26" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">     PYBUILD_SYSTEM=custom \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">     PYBUILD_TEST_ARGS="PATH=$(CURDIR)/build/scripts-2.7:$$PATH $(MAKE) test" \</span>

</pre>

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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext">       dh_auto_test</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="29" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">endif</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" 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">override_dh_auto_clean:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="LC33" class="line" lang="plaintext">     dh_auto_clean</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

<a href="https://salsa.debian.org/med-team/pbh5tools/compare/b1343d6bd06db3eb08e689a0732a2f1e54469026...7c969ccec60aa22eb7735e988967e18e2fbc0a0a#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.rst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,14 @@ To install ``pbh5tools``, run the following command from the ``pbh5tools`` root</td>

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<td class="diff-line-num old_line" 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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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="plaintext">   python setup.py install</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="LC30" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext">If you do not have `root` or `sudo` permissions, you can install locally by:  </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">1. Installing pysam, numpy, Cython, and h5py to your home directory.  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">              pip install --user --upgrade numpy h5py pysam cython</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">2. Running </span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">              python setup.py install --user</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">####################</span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Tool: bash5tools.py</span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">####################</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" 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="88" 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">@@ -80,10 +88,10 @@ Usage</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">Examples</span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">--------</span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Extracting all <span class="idiff left right">Raw</span> reads from ``input.bas.h5`` without any filtering</span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">and exporting to <span class="idiff left right">FASTA (``myreads.fasta``)</span>: ::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Extracting all <span class="idiff left right">subreads</span> reads from ``input.bas.h5`` without any filtering</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="plaintext">and exporting to <span class="idiff left right">a FASTA file named ``myreads.fasta``</span>: ::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">    python bash5tools.py <span class="idiff left right">input.bas.h5 --outFilePrefix myreads --outType fasta --readType Raw</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">    python bash5tools.py <span class="idiff left right">--outFilePrefix myreads --outType fasta --readType subreads input.bas.h5</span></span>

</pre>

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95

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="88" 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">

88

</td>

<td class="diff-line-num new_line" data-linenumber="96" 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">

96

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">Extracting all CCS reads from ``input.bas.h5`` that have read lengths</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="89" 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">

89

</td>

<td class="diff-line-num new_line" data-linenumber="97" 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">

97

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">larger than 100 and exporting to FASTQ (``myreads.fastq``): ::</span>

</pre>

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