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Commits on Oct 4, 2016

• merging in master

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• removing inline completely

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Commits on Mar 18, 2016

• Merge pull request #30 from udo-stenzel/master

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• Merge pull request #33 from samdemorest/master

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Commits on May 23, 2015

• Merge pull request #28 from alliemacleay/master

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Commits on May 19, 2015

• Merge pull request #26 from alliemacleay/master

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Commits on Jan 7, 2015

• Merge pull request #21 from alexpreynolds/clang-patch

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Commits on Feb 10, 2014

• adding a tag for the latest version for homebrew

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Commits on May 31, 2013

• added in checks to make sure that quality is above minimal threshold, and below maximal threshold

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Commits on May 30, 2013

• updates to check for quality scores too low/high during merging

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Commits on May 13, 2013

• Updates to readme, correction for specificity vs sensitivity.

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Commits on Feb 20, 2013

• fixing compiling issues on mac

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Commits on Sep 8, 2012

• Merge branch 'master' of github.com:jstjohn/SeqPrep

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• local changes to makefile?

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Commits on Mar 21, 2012

• Merge pull request #5 from DarwinAwardWinner/ldflags-fix

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Commits on Oct 25, 2011

• Merge branch 'master' of github.com:jstjohn/SeqPrep

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• local changes to seqlens

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Commits on Sep 15, 2011

• adding fastq-mcf results back into test and mentioning those on the readme

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• updating README with new test

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• Updated tests to double check that adapters are being trimmed from reads even when the adapter is only at the last few bases. It appears that the program is working nicely on this case.

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• reformatting README.md

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• Added option to save discarded reads into SeqPrep (Thanks @jdh237!). Also slightly modified default settings for trimming based on further sensitivity/specificity optimization on test data.

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Commits on Aug 30, 2011

• fixed a bug that results in quality scores higher than the maximum allowed quality score, also added a parameter to set the maximum quality that is output by the program when read merging happens

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Commits on Jul 7, 2011

• modifying the default parameters, the documentation to reflect those defaults, and posting a link to the website where I post the stats of adapter trimming sensitivity and specificity under differe…

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• updating test script to reflect the correct correct reverse adapter sequence

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• modifying readme to describe my strategy for finding the adapter sequence

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• updating documentation"

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• modification to calculation of sensitivity and specificity in test code, doesn't change much but is more correct now

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• fixing simulated data, and making parameters a little more stringent, the results are the same on the simulated data but it might be a little better with weird cases in real data now

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• updating readme

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• updating readme

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• adding in the shorter test files as well

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• adding lots of testing stuff, and updating defaults as a result of those tests

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Commits on Jul 6, 2011

• fixed a bug where resulting in high probability of discarding reads with low quality bases at the end

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Commits on Jul 5, 2011

• now trim parts of reads that do not overlap when performing adapter trimming as well as read merging

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