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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/scythe">Debian Med / scythe</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/f22a8910f63c8b80fc0953a5a93b7d5b5281f50e">f22a8910</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T03:22:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">intial import
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/4cb37f1952d117ee16f9b1190e63009c069c54f9">4cb37f19</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T03:23:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">error fixed in readme: scythe does not pick out 5'-end contaminants
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e61f86f475fab13af9eb4e11fe281042c8eb494e">e61f86f4</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T03:25:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added solexa 3'-end adapter sequences
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/30987f911c2678d89534c9fe7bcbc669051a572a">30987f91</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T03:28:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">version bump in README.md, added caveat about usage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/26f59b3535a144ff00ec467b223987c321bd299d">26f59b35</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T16:48:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed typo in readme (thanks peterjc for finding this)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/19b5c2d78b5ef37356ed44a05cb6a03b37453732">19b5c2d7</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T18:33:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">moved license, added more in readme, and enabled min match argument
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e94c79818f0f87b4a102a19d29a330327a871a1c">e94c7981</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T18:34:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed improper format in readme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/a8d06244d0e5b2e2bf8f8bd9b6551f8091b1f604">a8d06244</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-03T18:36:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more minor formatting changes to readme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/328d98bc2a687a4c157955da01d29e2a7acc7c93">328d98bc</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-16T00:29:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added sequence header tags an option, added O3 opt, refactored makefile, got rid of c++ style comments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5784292b3497ee8e9b6321f24d5a7ec357b998f6">5784292b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-02-16T00:31:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">resolved merge conflict from changes with min-match
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/37a8db0e42f4ca0e2466b73466198d1e0e26fc8c">37a8db0e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-04-12T23:06:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed 5' code, which scythe will maybe handle later
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/acc1c0f953a24fea1576e32a30eb28d8aba87c07">acc1c0f9</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-04-12T23:12:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">nicer handling of not found FASTQ files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/df5cf08b542ef40f0615daec535d23da36d35202">df5cf08b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-04-13T01:13:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed unnecessary enum
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/4ffefaadabd5c4900ffc43c017c42cc8b9558950">4ffefaad</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-05-28T23:38:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug that occurred when FASTA headers didn't have a space, added PHRED qualities, added quality info to usage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c3bd0105de62b7827e610647a1ec895af14cc59a">c3bd0105</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-05-28T23:42:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reformatted usage string to support ISO C90 fputs max length requirements
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/3751569386bd1939a1a31356c19cfd64aac7641c">37515693</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-05-30T03:15:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug in quality to probability conversion, added solexa conversion too
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/f865cd474f9a3f33687236d2fc4cdf63b28dc28a">f865cd47</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-05-30T03:25:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added note about min-match default change
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8472bb2ab2c1cdf460551c6ba75a01e3e6d22fa9">8472bb2a</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-05-30T03:31:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated qrqc url
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fb82722b23295277fc1be2a835e65f5fe4f606ca">fb82722b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-06-01T20:19:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">version bump
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c7d6350e570e14908012d7153b9658d0db8d07a1">c7d6350e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-25T17:51:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added read sim
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2712654396f1fba4e4ae369a7461b3116d9559dd">27126543</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-25T17:52:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">touched read sim
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9aea85f0abfd61efd891d3e1413bea016030c20f">9aea85f0</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-26T00:28:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">read simulation for testing added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5c4f53240fd916a665b1d43d9024dc994c7c2c01">5c4f5324</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-26T00:37:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed second FASTQ header issue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/3fb06d16bb58d3ab427bc90b7b45ad9f328d78a6">3fb06d16</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T16:39:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">finished read-sim.R, added results-parsing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2b8d7c9baca1105e538d1a7f543b62504517e3ac">2b8d7c9b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T19:09:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added prob base correct reporting to matches.txt
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ee544363bb4e6ec55f1419b06da82dbde11dd411">ee544363</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T19:09:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branches 'test' and 'master'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fa64982976740e94fc2a673b36cff37a18c7af7f">fa649829</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T20:50:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added quality reporting to matches.txt and parsing in results_parse.py
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/02664e2bb2e2f233fa5156a63171addd24c82100">02664e2b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T23:13:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added R script to run tests and create ROC curve
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/43bfc67ae07691c2f82b247eed66d2eef03d23e7">43bfc67a</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-07-27T23:40:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor roc curve changes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/3bc8d125da521e0558e5baceb39145f2dd4476fd">3bc8d125</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-10T21:25:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bug with FN, added lattice based graphics for ROC curves
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/7516fbc68880f5dba1344fa86df761b9fd20f725">7516fbc6</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-16T17:57:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added code to save roc plot
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/493d0059fc940c9f15e569f8f73912fcd25768b3">493d0059</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-16T21:17:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor bug fix; FAQ added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/174796ca51159a92409d30456a05807fb7f8111e">174796ca</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-16T21:28:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor readme correction
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8d848960e32c99ee47e757b81ab9edc1cf24859f">8d848960</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-16T21:53:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed output from stdout; moved to stderr so > works.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/abb4d523f8afa56c13d0c7dda8ea631a00ca78bc">abb4d523</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-16T21:54:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">documentation correction in FAQ
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/96948736dca02f2c412dbf111fee39a14a6ab9cf">96948736</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-17T20:50:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">corrected minor bug/typo
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/f4fbae5d28e0f861b093732a6fa1e8239e56fdd6">f4fbae5d</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-25T01:40:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">minor bug fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/4c508553c2acd3e8010847a4dee9b518f63d1d73">4c508553</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-25T01:41:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added contam diff measures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/d378629f6d5369511d78a478bb18935ae1d7e50e">d378629f</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-25T01:41:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of github.com:vsbuffalo/scythe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c9670c604bbb2a5e138ee262b1e2072340666118">c9670c60</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-08-25T02:50:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">testing code checkin - still buggy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e76174ad8dc0f8bd5f37706f0f41a6830a368b00">e76174ad</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-09-29T18:02:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check in paper progress
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8d6d8977bb52cfa50c32943b2bb90ea67923e0f9">8d6d8977</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-09-29T18:07:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'testing'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/72800ff08e882e5f1f1a68bca0970b0e1be5e726">72800ff0</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-09-29T18:08:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of github.com:vsbuffalo/scythe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/01bb23a0d68221aeea9ea8d16faef04243ea4ef0">01bb23a0</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-09-29T23:46:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cleaned up some writing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fcdbb1fb7b23c76a96ac46123d52426f68da65cc">fcdbb1fb</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-01T01:27:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more updates to paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5d6fbcc52efdc10efbe1f3deeaf83a0987466c75">5d6fbcc5</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-03T19:56:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new generic comparison file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/716e83cb133f13fa09ef9ffddf957d2b2a25e542">716e83cb</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-04T21:52:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more testing code added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/760a6b657d58d4f346ad38f67ba5892c6702e77a">760a6b65</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-28T21:29:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new bounds checking for qualities
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/612b725ac4146f66f6d8f8a990fc5f40427d32b1">612b725a</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-28T21:36:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">made error messages more consistent
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e778eea4c151121f5a1e98b612e66de57f015829">e778eea4</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-10-28T21:39:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added func prototype to avoid GNU/Linux build warning
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/d66ec19854b3e078b7518beced46d97818be4606">d66ec198</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-12-19T22:17:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new version of compare.py with hashing on heades
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e09168a28eb8eaddf3e13fb4685be34cdebe4ee9">e09168a2</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2011-12-19T23:48:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added output info on left out reads with trimmer
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/0b6ae5b2d38123b2a76ce8f96abd4bb3f69aae00">0b6ae5b2</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-01-05T19:20:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">uncommented code out, for entire new run
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/3995b85b6fa8fecd0e368235fb7b47a106802a7a">3995b85b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-01-05T19:22:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added testing files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/54af8fe100aeb87a968b5a70c221d5221bb6efd2">54af8fe1</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-01-05T21:33:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added read simulation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e89d1802f9051499faedaca63e6228156be1cdd2">e89d1802</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-02-19T00:20:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">updated scythe's output of headers so that it writes full header string
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/53ba45f03267fa94277b165a03bce86d2e411917">53ba45f0</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-02-19T00:26:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">version bump
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/556ff2b1d3436672bd2b2413202f072cfd0be12a">556ff2b1</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-02-19T00:43:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">udpated readme
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/133fc91cebee759c2920176dfc168028860d416b">133fc91c</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-03-02T21:53:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">increased max adapters to 1000
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fcc06c14d1803dc55d952f4db871758e78beccec">fcc06c14</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-03-08T22:05:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">paper edits, removing lost of materials to shift to sup materials
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/d4adae96994434ff7db8e9ceea9156da6592523b">d4adae96</a></strong>
<div>
<span>by Joseph Fass</span>
<i>at 2012-03-14T00:41:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">revamped adapter sequences
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/535b6387dd771d8f68317912773023c965eabb4e">535b6387</a></strong>
<div>
<span>by Joseph Fass</span>
<i>at 2012-03-14T00:49:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added adapter+barcode instructions to README.md
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/b20c02bd1608324046d2766bc8001c0cc05bbac5">b20c02bd</a></strong>
<div>
<span>by Joe Fass</span>
<i>at 2012-03-14T20:49:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">edited README and adapter files for legal reasons
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/51608bd7e478d2f0d3c1830f268998e7a3f16a80">51608bd7</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-21T00:16:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added btrim adapters for testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/f5b50218a02ce16673fea4c1404f16c39d9364a3">f5b50218</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-21T00:36:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed bugs to testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5c487dabe5181eb45d0e4b59caddbf3e6e116eb2">5c487dab</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-23T19:17:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added new R analysis file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ce1d1ecd1e3db7726b01e0de1f17412f4839208a">ce1d1ecd</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-24T01:40:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more extensive testing in R
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/1ea9ff770a669759d011f9227d523835a52fdc72">1ea9ff77</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-25T00:19:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">file processing mostly working
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/db86ebb89f53cf65bb6010cb84c71e0ed7e1f7e2">db86ebb8</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-25T19:28:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">split d
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ae54cbaaf41b0377a5eab9b1eb78a3c60d10011e">ae54cbaa</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-30T20:31:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed testing so that stats calculated earlier
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2e4109219bce1518429cb184d247694ab6e93cb7">2e410921</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-04-30T23:27:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ggplot roc curve of results
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fc3657240b24195c3809ce1027e8ceaa0c6cec88">fc365724</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T00:10:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ggplot image save and fixed btrim options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e7b2195df370bd60da1b151ac3ce84e504b53603">e7b2195d</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T00:34:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">massive refactor to get new-testing changed to testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6593b97357ba8a3d99ed9e0177d42c7236ccab8a">6593b973</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T01:15:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">multiple contam rate testing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/f6bafd1daa904f95a1cb965ddecc2d1d1514ff71">f6bafd1d</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T03:12:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">changed program to var
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/14f308739c8b9844690e155ee93eacb060f021ad">14f30873</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T03:21:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed Makefile targets
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/1a6823ef5739ef38f35d0d50f3e91345551f847c">1a6823ef</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T18:35:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added incorrect length stats
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fbd2c0089a39593519fe096789690563c65ad1e7">fbd2c008</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T23:13:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added refs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8361197b3eb7fb478f119d17fa9556eb3f2beede">8361197b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T23:14:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of github.com:vsbuffalo/scythe
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2bb72f9d7098e46707a642f1e0026a7f5779a29b">2bb72f9d</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-01T23:36:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added Bioinformatics Journal style
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ecce9f988418be9b9b09b841b54f0a2651574fd2">ecce9f98</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-02T01:27:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">additions to paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/3f1ec014048f8a724f955ae2360f486d791f7741">3f1ec014</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-02T21:53:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more paper additions, graphics, and supplementary materials
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/561e6c8eac1769b28bf2aab9436c517989a08770">561e6c8e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-03T00:48:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more additions to paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/33784fb60415c8f0906bcbe4b4be5cfd906bf9b8">33784fb6</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-03T19:53:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">few edits to paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/0e29b024c25736ad2381d3a9109f04f2cea93661">0e29b024</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-03T20:12:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">editing paper down in size
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/667e56a56c5731114fd5c8c3ab30d37630a43f55">667e56a5</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-03T20:17:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r package citations added
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5cef1e9a0e3fce8ad9c5f084e88993fde6a3f361">5cef1e9a</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-05-04T18:36:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed some minor errors in paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/26addb6458199fe7ee79990161a88af3b9ea736b">26addb64</a></strong>
<div>
<span>by Joseph Fass</span>
<i>at 2012-05-29T23:33:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replaced adapter files and added explanatory text to README
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/4e1d7a3141a107c7e031e7d5f7ba6f6193457a92">4e1d7a31</a></strong>
<div>
<span>by Joseph Fass</span>
<i>at 2012-05-29T23:47:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge remote branch 'upstream/master'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/872a54c996a1a9f5b3f5210d92bcbd8d7efcaa04">872a54c9</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-06-01T00:17:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #1 from jfass/master
revamped adapter files (one for older solexa adapters, one for Illumina's current TruSeq adapter), and added description of adapters and how to modify with barcodes</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c5c33e6c3d7db68e793fb04b54ca5efa062dae1e">c5c33e6c</a></strong>
<div>
<span>by mylons</span>
<i>at 2012-11-07T12:57:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Was getting this upon a fresh clone of the repo:
gcc -Wall -pedantic -DVERSION=0.981 -std=gnu99 -lz -lm match.o scythe.o util.o prob.o -o scythe
scythe.o: In function `ks_getc':
scythe.c:(.text+0x18a): undefined reference to `gzread'
scythe.o: In function `ks_getuntil':
scythe.c:(.text+0x289): undefined reference to `gzread'
scythe.o: In function `main':
scythe.c:(.text+0xc4b): undefined reference to `gzopen'
scythe.c:(.text+0x1024): undefined reference to `gzclose'
scythe.c:(.text+0x1044): undefined reference to `gzopen'
scythe.c:(.text+0x151a): undefined reference to `gzclose'
util.o: In function `ks_getc':
util.c:(.text+0x18a): undefined reference to `gzread'
util.o: In function `ks_getuntil':
util.c:(.text+0x289): undefined reference to `gzread'
prob.o: In function `qual_to_probs':
prob.c:(.text+0x129): undefined reference to `powf'
prob.c:(.text+0x1a8): undefined reference to `powf'
collect2: ld returned 1 exit status
make: *** [build] Error 1
Comments in this thread led me to this solution: moving the $(LDFLAGS) after the
sources ensures some linux compatibility
http://stackoverflow.com/questions/9145177/undefined-reference-to-gzopen-error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/24b6710fc9927ec2860c345c86133bf6887979d3">24b6710f</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-18T10:12:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #8 from mylons/master
Possible Makefile linux compatibility issue</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/b24583cfb1257903384c0db7b2f7e9c13cfba9a4">b24583cf</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-19T07:53:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initial new matching prototype
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9b623e2943842613bd267338979b893d11dd347d">9b623e29</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-19T09:51:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed formatting issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/285a7863aa740ce1b9ea32bcdc6788a72e17d454">285a7863</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-19T10:17:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">simplified comment output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e540bfc88ed58d7a7ec1106dd095022a617cd80c">e540bfc8</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-19T10:28:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added news, todo, new truseq seqs for test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6e21e87372160db1c77fb0c15aea72384ab7d432">6e21e873</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-19T11:37:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed heuristic which causes non-exhaustive search across adapters
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/141fcbfac68c80fc57a47362535e9ce39cabb6c8">141fcbfa</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-20T00:41:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">swapped for loops for safer matching with heuristic stopping point
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/45b91d3059ef9c6a2dec4dfba62dd7cbd7a8260f">45b91d30</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-20T01:07:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">commented out adapter occurence array; fixed mem leak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6ccdeb1eb15dd26998e7a6a2ff8fb6eb59a02463">6ccdeb1e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-20T01:12:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more mem leak fixing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/5657dfcbbbdcdae80e1555c0e5049c07430087f4">5657dfcb</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-20T02:14:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed another memory leak
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/18fa6c101c37210888f6d13ba52723add3391cfc">18fa6c10</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2012-12-21T00:06:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed double free issue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/7f49366e90521df687dd7c199367079757d97a1b">7f49366e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-03-27T22:07:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">merge of experimental branch that does full seq matching
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/29ac0e56f19d17f4cd1d8024211036306a44547c">29ac0e56</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-03-27T22:17:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed typo in readme (thanks JRI), updated with new matching algo from merge in previous commit; version bump
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9f3b86aa412fc207da7073b28ec6b6f144a77a83">9f3b86aa</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-03-28T19:34:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">increased default prior; tests show this is a better choice
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ffd69027e099e8eeb34c88d61215510ad59aa0ef">ffd69027</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-04-14T01:00:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">replace empty lines with Ns
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6e1ba55ec20396bbe11125b9d3d85d66d703e518">6e1ba55e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-04-14T01:55:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed issue with shift
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/ffc7767c18e194b70707bcd364491f37a36c9e75">ffc7767c</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-04-14T01:57:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed opt flag
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c94f130b02dcd6dfe127f016da020da77e2ed1c2">c94f130b</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-04-14T02:17:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed min_keep parameter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/cb0695a76f101fb0f4adfd0c33c07c682b426092">cb0695a7</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-04-14T02:21:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added note about min_keep in readme, fixed makefile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/dd95ac427485fc5acf0cae3d6f7b9002d3775b85">dd95ac42</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-05-11T20:05:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added makefile targets for libscythe.so; cleaned up other parts of Makefile
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/0410cc0cd56a07890a8ca5093f873874a46480b1">0410cc0c</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-06-13T20:03:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">modified makefile so that it can find zlib
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/fb3114743e59c6255b2f2a3bacced9816aef46fe">fb311474</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-07-22T23:57:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added option for stdin processing
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2b84e28e96141a0ccbea474a498c45770a97412a">2b84e28e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-09-30T18:32:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed compiler warnings from Linux gcc 4.7.3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/b459381f7adf09ed66097d0fab0f1a23c463b0b6">b459381f</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-09-30T18:36:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added two other adapters
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c5548d1197216dcea06cfbbb9b83b165b03773ac">c5548d11</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-09-30T19:09:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new minimal (non-redundant set of adapter)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6a51b6daba7d238c04973a2ab36c2b2266bf6f61">6a51b6da</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-09-30T19:21:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new adapter proposal
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/dd8f8d8d3b334c7bc73e2ed505da168d80e176f4">dd8f8d8d</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-09-30T20:02:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">jnfass's additions, without truncated cases
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/eedd2e30957edec1cbf7888896b7e71eb0404e67">eedd2e30</a></strong>
<div>
<span>by Yaron de Leeuw</span>
<i>at 2013-11-27T09:57:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix the adapter in the matches report.
Saved the current adapter index in best_adapter
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9b965ee399a18caf1f96e433f78d405620e3a1df">9b965ee3</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2013-12-16T18:56:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #13 from jarondl/fix_matches_report
Fix the adapter in the matches report.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9b280401f8330e15b7ca9fb73b8942f50baf31ba">9b280401</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-02-08T05:12:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed readme, changing makefile readme to all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/d773d96fd51e718c96dbf13d24ba58fa4e3d3cb5">d773d96f</a></strong>
<div>
<span>by Richard Feltstykket</span>
<i>at 2014-04-04T21:58:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Typo fix in libscythe.so target, LDFLAGS order fix in all targets.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/9b40df7f2507a7244991c7fef43407c6b8c74d9b">9b40df7f</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-05T18:56:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #16 from rjacobsen/master
Typo fix in libscythe.so target, LDFLAGS order fix in all targets.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6c6e6a6d2e819d2425ae72d19bf8af53491ccbb8">6c6e6a6d</a></strong>
<div>
<span>by Kevin Murray</span>
<i>at 2014-04-14T04:50:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">small optimisations to match functions & sum
Mangaged to decrease runtime to ~75% of what it was with some simple
optimisations. md5sums of output appear the same
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/d3712b9757f0848865f308f5365c0f3dded73174">d3712b97</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-14T06:19:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">version bump
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8bfe3c6ebc4045ae15da9f06ab0415ae04da36aa">8bfe3c6e</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-14T06:20:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/6d92a57e2c13734f9a6bfd3b946d08c9aba10eb1">6d92a57e</a></strong>
<div>
<span>by Kevin Murray</span>
<i>at 2014-04-14T06:33:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">further optimisations which reduce num of allocs
Basically trying to remove the number of calls to alloc by preserving
the score array for the duration of the call to find_best_match
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/369cd64b0befacfa62ac13fcf25304a245d0b43d">369cd64b</a></strong>
<div>
<span>by Kevin Murray</span>
<i>at 2014-04-14T06:41:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">[scythe.c] fix to fclose output_fp w/ -o option
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/7c4978378065662e785c4ecc422e082728af4fb0">7c497837</a></strong>
<div>
<span>by Kevin Murray</span>
<i>at 2014-04-14T06:48:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update tests w/ optimised score_sequence API
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/8ffdb67fd32eb9755593a8860a718ba67bb101ac">8ffdb67f</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-19T19:53:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #18 from kdmurray91/optimised
Further optimisations</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/2aad12e0207072a14771a351979cce635105d1e9">2aad12e0</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-19T19:53:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge pull request #19 from kdmurray91/fix-fclose
Call fclose on output_fp when -o option is given</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/c128b19c65961d1e5ef177919f74d4f533aa4f5d">c128b19c</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-04-19T19:59:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">version bump; removed paper, this will go into separate repository
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/20d3cff7d7f483bd779aff75f861e93708c0a2b5">20d3cff7</a></strong>
<div>
<span>by Vince Buffalo</span>
<i>at 2014-10-17T21:11:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixed error in readme, thanks to @kbradnam
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/bf847cbab9b038a7fc372401374e919325620bdf">bf847cba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T14:25:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.994+git20141017.20d3cff</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/e5a8da6b338b1f4ec68dd075395a2eaa86f5e9c0">e5a8da6b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:49:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use git mode
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/122ccade891f9e369de0bfd0b92c2fc919562e20">122ccade</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:49:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.994+git20141017.20d3cff</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/b5103f93528b56164648239a1d54fb88b17fa253">b5103f93</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:49:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.994+git20141017.20d3cff'
Update to upstream version '0.994+git20141017.20d3cff'
with Debian dir 4b8ec7504aaa2a6119c2b2049cb1ef77b4071394</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/caac4ccc3e6d2896186e01db1e8fe2476755d164">caac4ccc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:50:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unneeded get-orig-source target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/119f4895430f6f160737c493cd7817ff501d1984">119f4895</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:50:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/09055c8b2c93d3240dddf9d84e58986d3922fc03">09055c8b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:50:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/420c15fb6f01da052e6bce7b9e098813dcdc4b56">420c15fb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:50:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scythe/commit/409da38feb6eebfaa307f0bc4448f783db030997">409da38f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-24T15:51:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,12 +42,5 @@ tramp</td>
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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">*.out</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
43
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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
43
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">scythe</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">test-scythe</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">*.gch</span></pre>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"># debian stuff</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">debian/files</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">debian/scythe.substvars</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">debian/scythe.debhelper.log</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">README.html</span></pre>
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<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scythe (0.994+git20141017.20d3cff-1) unstable; urgency=medium</span>
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2
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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"> * d/watch: use git mode</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Drop unneeded get-orig-source target</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper 11</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.2.0</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 24 Aug 2018 17:50:51 +0200</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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1
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">scythe (0.994-4) unstable; urgency=medium</span>
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2
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">9</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">11</span></span></pre>
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<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,18 +3,19 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Kevin Murray <spam@kdmurray.id.au></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= <span class="idiff left right">9</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= <span class="idiff left right">11~</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python-markdown,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> check</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.7</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/git/debian-med/scythe.git</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/scythe.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.2.0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/scythe</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/scythe.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/vsbuffalo/scythe</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">Package: scythe</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Description: Bayesian adaptor trimmer for sequencing reads</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> Scythe uses a Naive Bayesian approach to classify contaminant substrings in</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> sequence reads. It considers quality information, which can make it robust in</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -6,7 +6,3 @@</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh_auto_build</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> markdown_py -f README.html README.md</span></pre>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">get-orig-source:</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> @echo "Downloading source from GitHub"</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> wget -O scythe_0.994.orig.tar.gz https://api.github.com/repos/vsbuffalo/scythe/tarball/20d3cff7d7f483bd779aff75f861e93708c0a2b5</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/scythe/compare/fa6b295a9f96ce44a5773e7e90e593dd7071c8fa...409da38feb6eebfaa307f0bc4448f783db030997#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#version=3</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">#https://github.com/vsbuffalo/scythe/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</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">opts="mode=git,pretty=0.994+git%cd.%h" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/vsbuffalo/scythe.git HEAD</span></pre>
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