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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 Mar 16, 2012

• Place LDFLAGS after OBJECTS in compile command

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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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• updating readme to reflect currently available options

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• adding the adapter trim help item back to the help documentation

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• making defaults more sensitive to adapters

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• changing makefile arguments

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• fixing a weird index issue that wasn't being handled properly

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• adding prettyprint for read overlap even when just doing adapter trimming for user debugging purposes

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Commits on Jul 2, 2011

• updating documentation to reflect help, and clarifying which adapters the defaults are in both the help and the program

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• adding warning about new line at the end of a file

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• reverting makefile to 03 optomization flags

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