kshakir ac3f1be7f0 Added a samtools merge CLF. ... Using samtools to merge the low pass bams before cleaning to avoid "Too many open files." with 1500+ bams. Other minor cleanup as pointed out by the IntelliJ scala plugin. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5942 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-03 22:20:38 +00:00
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core	new name to the pipeline, it's now in core, happy to support it.	2011-06-02 23:34:54 +00:00
examples	When /etc/mailname is unreadable fall back to the hostname.	2011-04-11 20:22:44 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.	2011-06-03 20:11:31 +00:00
playground	Added a samtools merge CLF.	2011-06-03 22:20:38 +00:00