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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-bx">Debian Med / python-bx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/-/commit/0c79fd8d9d2ac5b0a82b5e8e79e78fa6e22e23be">0c79fd8d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-18T06:34:52+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">B-D on python3-pytest-cython
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/-/commit/4a28bc532ecb1fb814bd0f08888d29367bc09b58">4a28bc53</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-18T12:25:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Re-diff, Re-enable shebang.patch
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-bx/-/commit/3203731742944fb8a351d0b1cf67359d4f3f5301">32037317</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-18T12:25:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#50d4a32d9f88409b9c1c42a8bdf7478212416bf0">
debian/patches/fix_BIN_OFFSETS_MAX
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#21f07864a3929c097dd38d0ed1d1b912b1f34a64">
debian/patches/shebang.patch
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-bx (0.8.13-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-bx (0.8.13-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="new_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Build-Depends: s/nose/pytest/</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 17 Feb 2022 20:35:53 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * B-D on python3-pytest-cython</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Re-diff, Re-enable shebang.patch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 18 Feb 2022 12:05:03 +0530</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">python-bx (0.8.9-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-all-dev:any,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-lzo,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python3-pytest-cython <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3-numpy <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-six,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> cython3</span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301#50d4a32d9f88409b9c1c42a8bdf7478212416bf0"><strong>debian/patches/fix_BIN_OFFSETS_MAX</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ From: Michael R. Crusoe <michael.crusoe@gmail.com></td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: fix error for 32bit systems</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/interval_index_file.py</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/interval_index_file.py</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -123,7 +123,7 @@</span><span class="idiff left right"> for i in range(BIN_LEVELS - 2):</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -123,7 +123,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> BIN_OFFSETS_MAX.insert(0, (BIN_OFFSETS_MAX[0] << BIN_NEXT_SHIFT))</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> # The maximum size for the top bin is actually bigger than the signed integers</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> # we use to store positions in the file, so we'll change it to prevent confusion</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Subject: fix error for 32bit systems</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> # Constants for the minimum and maximum size of the overall interval</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> MIN = 0</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -136,12 +136,14 @@</span><span class="idiff left right"> def offsets_for_max_size(max_size):</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -136,12 +136,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> """</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> Return the subset of offsets needed to contain intervals over (0,max_size)</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> """</span>
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<a href="https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">#</span>shebang.patch</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">shebang.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_BIN_OFFSETS_MAX</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301#21f07864a3929c097dd38d0ed1d1b912b1f34a64"><strong>debian/patches/shebang.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/bed_build_windows.py</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/bed_build_windows.py</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/bed_build_windows.py</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/intervals/operations/subtract.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/intervals/operations/subtract.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" 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="LC6" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> Subtract one set of genomic intervals from another (base-by-base or whole</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> intervals). The returned GenomicIntervals will be in the order</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/bed_score_aligned_pwm.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/bed_score_aligned_pwm.py</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> Returns all positions of a maf with any pwm score > threshold</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> The positions are projected onto human coordinates</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/bed_score_aligned_string.py</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/bed_score_aligned_string.py</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> Returns all positions of a maf with any pwm score > threshold</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> The positions are projected onto human coordinates</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/maf_select_motifs.py</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/maf_select_motifs.py</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" 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="LC30" class="line" lang="diff"> """</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> Returns all positions of a maf with any pwm score > threshold</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> The positions are projected onto human coordinates</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/position_weight_matrix.py</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/position_weight_matrix.py</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" 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="LC37" 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="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> import math</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/pwm_score_motifs.py</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/pwm_score_motifs.py</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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<pre style="margin: 0;">+<span id="LC45" 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="LC46" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> Build windows of length `window_size` over the sequences defined by</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/bed_complement.py</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/bed_complement.py</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/bed_complement.py</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> Returns all positions of a maf with any pwm score > threshold</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> The positions are projected onto human coordinates</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/pwm_score_positions.py</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;">+++ b/lib/bx/pwm/pwm_score_positions.py</span></span>
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15
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" 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="LC54" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> Returns all positions of a maf with any pwm score > threshold</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> The positions are projected onto human coordinates</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/aggregate_scores_in_intervals.py</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/aggregate_scores_in_intervals.py</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" 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="LC61" 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="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> Given a list of intervals in BED format (`interval_file`) and a set of scores</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/align_print_template.py</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/align_print_template.py</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> """</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> Read an alignment from stdin and for each block print the result of</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/axt_extract_ranges.py</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/axt_extract_ranges.py</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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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;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC77" 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="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> """</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> Reads a list of intervals and an axt. Produces a new axt containing the</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/axt_to_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/axt_to_fasta.py</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> """</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> Application to convert AXT file to FASTA file. Reads an AXT file from standard</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> input and writes a FASTA file to standard out.</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/axt_to_lav.py</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/axt_to_lav.py</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> """</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> Application to convert AXT file to LAV file. Reads an AXT file from standard</span>
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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;">--- a/scripts/axt_to_maf.py</span></span>
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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;">+++ b/scripts/axt_to_maf.py</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> """</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> Application to convert AXT file to MAF file. Reads an AXT file from standard</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_bigwig_profile.py</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_bigwig_profile.py</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> """</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> Create a site profile vector showing the average signal accumulated from a</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_build_windows.py</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_build_windows.py</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> """</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> Build windows of length `window_size` over the sequences defined by</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_complement.py</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_complement.py</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> </span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> """</span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> Complement the regions of a bed file. Requires a file that maps source names</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/bed_count_by_interval.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/bed_count_by_interval.py</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/bed_count_by_interval.py</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_count_by_interval.py</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_count_by_interval.py</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python<span class="idiff left right">2.4</span></span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> """</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> For each interval in `bed1` count the number of intersecting regions in `bed2`.</span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/bed_count_overlapping.py</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/bed_count_overlapping.py</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/bed_count_overlapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_count_overlapping.py</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_count_overlapping.py</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python<span class="idiff left right">2.4</span></span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="diff"> """</span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"> For each interval in `bed1` count the number of intersecting regions in `bed2`.</span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/bed_rand_intersect.py</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></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;">--- python-bx.orig/scripts/bed_rand_intersect.py</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;">+++ python-bx/scripts/bed_rand_intersect.py</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_coverage.py</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_coverage.py</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> </span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> """</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> Print number of bases covered by all intervals in a bed file (bases covered by</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_coverage_by_interval.py</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_coverage_by_interval.py</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> """</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> For each interval in `bed1` print the fraction of bases covered by `bed2`.</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_diff_basewise_summary.py</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_diff_basewise_summary.py</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> """</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> Given two bed files print the number of bases covered 1) by both, 2) only by</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_extend_to.py</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_extend_to.py</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> </span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> """</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> Read BED file and extend each record to the specified minimum length. If chromosome</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_intersect.py</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_intersect.py</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> """</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> Find regions of first bed file that overlap regions in a second bed file. The</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_intersect_basewise.py</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_intersect_basewise.py</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> </span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> """</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> Find regions of first bed file that overlap regions in a second bed file. This</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_merge_overlapping.py</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_merge_overlapping.py</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> </span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> Merge any overlapping regions of bed files. Bed files can be provided on the</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_rand_intersect.py</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_rand_intersect.py</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC204" 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="LC205" 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="LC206" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="diff"> """</span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="diff"> From a set of regions and two sets of intervals inside those regions</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/div_snp_table_chr.py</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/div_snp_table_chr.py</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/div_snp_table_chr.py</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bed_subtract_basewise.py</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/bed_subtract_basewise.py</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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<pre style="margin: 0;">+<span id="LC212" 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="LC213" 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="LC214" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> Find continuous regions that are covered by the first bed file (`bed_file_1`)</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/bnMapper.py</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;">+++ b/scripts/bnMapper.py</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> """Map features from the target species to the query species of a chain alignment file.</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> This is intended for mapping relatively short features such as Chip-Seq</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/div_snp_table_chr.py</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/div_snp_table_chr.py</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC228" 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="LC229" 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="LC230" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="diff"> """</span>
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60
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="diff"> FIXME!</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/int_seqs_to_char_strings.py</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/int_seqs_to_char_strings.py</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/int_seqs_to_char_strings.py</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/find_in_sorted_file.py</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/find_in_sorted_file.py</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> Extract ranges of scores from a sorted file in which each line contains a</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/get_scores_in_intervals.py</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/get_scores_in_intervals.py</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC244" 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="LC245" 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="LC246" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> """</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> Read scores in "wiggle" format from `score_file` and intervals in "bed" format</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;">--- a/scripts/int_seqs_to_char_strings.py</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/int_seqs_to_char_strings.py</span></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC252" 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="LC253" 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="LC254" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="diff"> """</span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="diff"> Translate lists of space separated integers (magnitude less than 62) and print</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/interval_join.py</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/interval_join.py</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/interval_join.py</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/interval_count_intersections.py</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/interval_count_intersections.py</span></span>
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> """</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> Read two lists of intervals (with chromosomes) and count the number of entries</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/interval_join.py</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/interval_join.py</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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78
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="diff"> </span>
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79
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="diff"> """</span>
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80
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="diff"> Match up intersecting intervals from two files. This performs a "full join",</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/lzop_build_offset_table.py</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/lzop_build_offset_table.py</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/lzop_build_offset_table.py</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/lav_to_axt.py</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/lav_to_axt.py</span></span>
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85
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> """</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> Application to convert LAV file to AXT file. Reads a LAV file from standard</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> input and writes a AXT file to standard out; some statistics are written</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/lav_to_maf.py</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/lav_to_maf.py</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> """</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> Application to convert LAV file to MAF file. Reads a LAV file from standard</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> input and writes a MAF file to standard out; some statistics are written to</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/line_select.py</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/line_select.py</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> </span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> """</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> Read a file containing a 0 or 1 on each line (`feature_file`), output</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/lzop_build_offset_table.py</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/lzop_build_offset_table.py</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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87
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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88
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="diff"> </span>
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89
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="diff"> """</span>
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90
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="diff"> Read a compressed file as created by 'lzop' from stdin and write a table to</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/mMK_bitset.py</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/mMK_bitset.py</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/mMK_bitset.py</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/mMK_bitset.py</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/mMK_bitset.py</span></span>
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95
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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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;">-#!/usr/bin/env python<span class="idiff left right">2.4</span></span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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97
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309
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<pre style="margin: 0;"> <span id="LC309" 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="LC98" class="line" lang="diff"> from __future__ import print_function</span>
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99
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="diff"> </span>
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="diff"> from optparse import OptionParser</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/maf_div_sites.py</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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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;">--- python-bx.orig/scripts/maf_div_sites.py</span></span>
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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;">+++ python-bx/scripts/maf_div_sites.py</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> </span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_build_index.py</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_build_index.py</span></span>
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105
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> """</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> Build an index file for a set of MAF alignment blocks.</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_chop.py</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_chop.py</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> </span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> """</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> Chops alignments in a MAF file to piece of a specified length. A random set of</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_chunk.py</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_chunk.py</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> </span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> """</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> Read a MAF from stdin and break into several new mafs containing no more than</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_col_counts.py</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_col_counts.py</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> """</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> For every column that occurs in a multiple alignment print the column</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_col_counts_all.py</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_col_counts_all.py</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> """</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> For every column that occurs in a multiple alignment print the column</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_count.py</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_count.py</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> </span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> """</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> Read a MAF from standard input and print counts of alignments, bases, or</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_covered_ranges.py</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_covered_ranges.py</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> """</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> usage: %prog species1,species2,... nrequired < maf</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_covered_regions.py</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_covered_regions.py</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> </span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> """</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> Read a maf file and print the regions covered to a set of bed files (one for</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_div_sites.py</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_div_sites.py</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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108
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="diff"> """</span>
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109
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="diff"> Create a bed file listing all the divergent sites between two specific species</span>
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110
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="diff"> in a maf.</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/maf_interval_alignibility.py</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/maf_interval_alignibility.py</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/maf_interval_alignibility.py</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_drop_overlapping.py</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_drop_overlapping.py</span></span>
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115
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" 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="LC390" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> Remove any blocks from a maf that overlap any of a set of intervals.</span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_extract_chrom_ranges.py</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_extract_chrom_ranges.py</span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> </span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> """</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> Reads a list of intervals and a maf. Produces a new maf containing the</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_extract_ranges.py</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_extract_ranges.py</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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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;">-#!/usr/bin/env python</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> </span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> """</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> Reads a list of intervals (start, stop) and a maf. Produces a new maf</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_extract_ranges_indexed.py</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_extract_ranges_indexed.py</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> """</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> Reads a list of intervals and a maf. Produces a new maf containing the</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_filter.py</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_filter.py</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> </span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> """</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> Filter each block in a maf file. Can filter blocks for a minimum number of</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_filter_max_wc.py</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_filter_max_wc.py</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> """</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> Filter maf blocks for presence of wildcard columns. Blocks must meet the</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_gap_frequency.py</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_gap_frequency.py</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> </span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> Read a MAF from standard input and print the fraction of gap columns in</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_gc_content.py</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_gc_content.py</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC444" 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="LC445" 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="LC446" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> Read a MAF from standard input and print average GC content of each alignment</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_interval_alignibility.py</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_interval_alignibility.py</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC452" 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="LC453" 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="LC454" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="diff"> """</span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="diff"> WARNING: bz2/bz2t support and file cache support are new and not as well</span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: python-bx/scripts/maf_species_in_all_files.py</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-bx.orig/scripts/maf_species_in_all_files.py</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-bx/scripts/maf_species_in_all_files.py</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_limit_to_species.py</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_limit_to_species.py</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.4</span></span>
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<pre style="margin: 0;">+<span id="LC460" 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="LC461" 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="LC463" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> Read a maf file from stdin and write out a new maf with only blocks having all</span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_mapping_word_frequency.py</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_mapping_word_frequency.py</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" 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="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>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_mask_cpg.py</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_mask_cpg.py</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> Mask out potential CpG sites from a maf. Restricted or inclusive definition</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_mean_length_ungapped_piece.py</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_mean_length_ungapped_piece.py</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> </span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> """</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> Read a MAF from standard input and determine the mean length of ungapped pieces</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_percent_columns_matching.py</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_percent_columns_matching.py</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> </span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> """</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> Read a PAIRWISE maf from stdin and print the fraction of columns whose bases</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_percent_identity.py</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_percent_identity.py</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> </span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> """</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> Read a PAIRWISE maf from stdin and print the percent identity of each</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_print_chroms.py</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_print_chroms.py</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> </span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> """</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> Read a maf from stdin and print the chromosome number for each alignment. It</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_print_scores.py</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_print_scores.py</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> </span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> """</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> Read a MAF from standard input and print the score of each block. It can</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_randomize.py</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_randomize.py</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> </span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> """</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> Randomize the order of blocks in a MAF file. If `sample_size` is specified,</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_region_coverage_by_src.py</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_region_coverage_by_src.py</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> Reads a list of intervals and a set of indexed mafs. For each interval print</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_select.py</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_select.py</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> </span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> """</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> Read a feature file containing a 0 or 1 on each line, output</span>
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545
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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/scripts/maf_shuffle_columns.py</span></span>
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546
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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/scripts/maf_shuffle_columns.py</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC548" 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="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> </span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> """</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> Randomly shuffle the columns of each block of a maf file. Note that this does</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_species_in_all_files.py</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_species_in_all_files.py</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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127
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="diff"> </span>
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129
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="diff"> """</span>
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="diff"> Takes a list of maf filenames on the command line and prints a comma separated</span>
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561
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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/scripts/maf_split_by_src.py</span></span>
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562
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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/scripts/maf_split_by_src.py</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> </span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"> """</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> Read a MAF from stdin and break into several mafs based on the source of</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_thread_for_species.py</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_thread_for_species.py</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> </span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> """</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"> Read a maf file from stdin and write out a new maf with only blocks having all of</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_tile.py</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_tile.py</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> </span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> """</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> 'Tile' the blocks of a maf file over each of a set of intervals. The</span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_tile_2.py</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_tile_2.py</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" 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="LC590" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> 'Tile' the blocks of a maf file over each of a set of intervals. The</span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_tile_2bit.py</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_tile_2bit.py</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" 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="LC598" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> """</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> 'Tile' the blocks of a maf file over each of a set of intervals. The</span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_to_axt.py</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_to_axt.py</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> """</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> Application to convert MAF file to AXT file, projecting to any two species.</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> Reads a MAF file from standard input and writes an AXT file to standard out;</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_to_concat_fasta.py</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_to_concat_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> </span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> """</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> Read a maf and print the text as a fasta file, concatenating blocks. A</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_to_fasta.py</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_to_fasta.py</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python.</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> """</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> Read a maf and print the text as a fasta file.</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_to_int_seqs.py</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_to_int_seqs.py</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> </span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> """</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> For each block in a maf file (read from stdin) write a sequence of ints</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_translate_chars.py</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_translate_chars.py</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> </span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"> """</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> Translate a maf file containing gap ambiguity characters as produced by</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_truncate.py</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_truncate.py</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" 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="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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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> Pass through blocks from a maf file until a certain number of columns</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/maf_word_frequency.py</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/maf_word_frequency.py</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> </span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> """</span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> Read a MAF and print counts and frequencies of all n-mers</span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/mask_quality.py</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/mask_quality.py</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC660" 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="LC661" 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="LC663" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> Masks an AXT or MAF file based on quality (from a binned_array) and</span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/nib_chrom_intervals_to_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/nib_chrom_intervals_to_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC668" 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="LC669" 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="LC671" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> Read a set of ranges and a nib file, print portions of nib overlapping</span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/nib_intervals_to_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/nib_intervals_to_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC676" 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="LC677" 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="LC678" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> """</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> Read a set of ranges and a nib file, print portions of nib overlapping</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/nib_length.py</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/nib_length.py</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> </span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> """</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> Print the number of bases in a nib file.</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/one_field_per_line.py</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/one_field_per_line.py</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> </span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> """</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> Read a file from stdin, split each line and write fields one per line to</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/out_to_chain.py</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/out_to_chain.py</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> </span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> import logging</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> import sys</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/prefix_lines.py</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/prefix_lines.py</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> </span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> """</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> Simple script to add a prefix to every line in a file.</span>
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713
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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/scripts/pretty_table.py</span></span>
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714
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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/scripts/pretty_table.py</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> </span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"> """</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"> Read some whitespace separated data from stdin and pretty print it so that</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/qv_to_bqv.py</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/qv_to_bqv.py</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> </span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> """</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> Convert a qual (qv) file to several BinnedArray files for fast seek.</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/random_lines.py</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/random_lines.py</span></span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> </span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> """</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> Script to select random lines from a file. Reads entire file into</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/table_add_column.py</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/table_add_column.py</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> </span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> """</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"> Tool for adding a column to a table. Expressions for the column are similar</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/table_filter.py</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/table_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"> </span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"> """</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> Tool for filtering a tabular data file. Fields are separated by tabs, the</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/tfloc_summary.py</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/tfloc_summary.py</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> </span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"> """</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"> Read TFLOC output from stdin and write out a summary in which the nth line</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/ucsc_gene_table_to_intervals.py</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/ucsc_gene_table_to_intervals.py</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> </span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> """</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"> Read a table dump in the UCSC gene table format and print a tab separated</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/wiggle_to_array_tree.py</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/wiggle_to_array_tree.py</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> </span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> """</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> Read data in UCSC wiggle format and write it to an "array tree" file.</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/wiggle_to_binned_array.py</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/wiggle_to_binned_array.py</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"> </span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"> """</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"> Convert wiggle data to a binned array. This assumes the input data is on a</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/wiggle_to_chr_binned_array.py</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/wiggle_to_chr_binned_array.py</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> </span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"> """</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> Writes compressed data from a wiggle file by chromosome.</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/wiggle_to_simple.py</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/wiggle_to_simple.py</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> </span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> """</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"> Read a wiggle track and print out a series of lines containing</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/bx/pwm/pwm_score_maf.py</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/bx/pwm/pwm_score_maf.py</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python2.4</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"> </span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> import sys</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> </span></pre>
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