1acf0f0b2c
Fixing bug in fasta .fai generation: trim the contig names to the first whitespace if one appears. We now generate indexes identical to samtools.
2012-08-29 22:36:27 -04:00
3253fc216b
FindBugs 'Maintainability' fixes
2012-08-16 15:53:06 -04:00
e923a2e512
Revving Picard to incorporate final version of ReadWalker performance improvements.
2012-01-10 12:12:33 -05:00
3642a73c07
Performance improvements for dynamically merging BAMs in read walkers.
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This change and my previous change have dropped runtime when dynamically merging 2k BAM files from 72.6min/1M reads to 46.8sec/1M reads.
Note that many of these changes are stopgaps -- the real problem is the way ReadWalkers interface with Picard, and I'll have to work with
Tim&Co to produce a more maintainable patch.
2011-12-16 09:37:44 -05:00
f3ad4ec94b
Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.
2011-07-27 22:06:23 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Eric Banks
Matt Hanna
Mark DePristo
David Roazen