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Commits on Feb 29, 2016

• fixed build for cori

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Commits on Nov 6, 2013

• refactored all system calls to go through ForkDaemon

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  5bbd699

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Commits on Nov 2, 2013

• fixed minor bugs

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Commits on Oct 30, 2013

• added ForkDaemon utility

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Commits on Oct 29, 2013

• minor changes

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  b46fa80

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Commits on Oct 16, 2013

• fixed mpi compiler warnings and build bugs

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  5e92418

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• fixed compiler warnings and build bugs

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Commits on Oct 5, 2013

• reduced debugging

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  0c9b2a6

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• fixed segfault

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Commits on Oct 4, 2013

• fixed quality scaling to account for fasta files properly

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• fixed comments on output reads and adjusted tests to reflect new comment structure

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  fc597d4

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• added qtrim recovery of remainder of the read

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Commits on Oct 3, 2013

• refactored artifact and quality filtering

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Commits on Oct 1, 2013

• reduced locking contention in recordAffectedRead

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Commits on Sep 30, 2013

• fixed ReadSetStream to auto-detect fastq quality (as best it can). Fixed runFilterTest and runMeraculousTest to account for quality scaling

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• fixed logic for fastq quality auto detect and scaling

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Commits on Sep 27, 2013

• removed FixPair app because I forgot what it was supposed to do

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Commits on Sep 26, 2013

• minor bug fixes

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Commits on Sep 11, 2013

• fixed newbler and cap3 to automatically shred long seed reads if over the respective read-size limits

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Commits on Sep 6, 2013

• added sampling and raw data output to TnfDistance

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Commits on Sep 5, 2013

• minor refactor of GenericHistogram

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  ec132b3

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• reduced verbosity

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  0cc4a2c

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• adjusted intra calculations to return likelihood functions of intra and inter distances

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Commits on Aug 30, 2013

• added RankVector unit test

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• fixed to error out if any OptionsErrorMessage is generated

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• added spearman distance as option to TnfDistance

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Commits on Aug 29, 2013

• reduced verbositiy of debug messages

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  82e1a16

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• minor fix to change normal thread reduction warning to debug message

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  2e5513a

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• added support for other sized kmers in TnfDistance

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Commits on Aug 28, 2013

• fixed buffer overrun in MPIBuffer

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Commits on Aug 16, 2013

• removed LRU caching for mmaped reads ( threaded race condition )

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Commits on Aug 13, 2013

• removed excessive debug output

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Commits on Aug 5, 2013

• access declarations are deprecated in favour of using-declarations

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Commits on Jul 31, 2013

• fixed assertions

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• added some costly assertions

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