asivache bfd6bf9ec5 PileupWalker just got a new option: --showIndelPileups. When this option is used, two lines are printed for every genomic location that has indels associated with it: first line is a conventional base pileup, the second line is an "extended event" (indel) pileup. The refence base in that second line is always set to "E" (for Extended), and the pileup string contains I,D,. symbols for insertion, deletion, noevent, respectively. Only this simple short format for indel pileups is implemented so far. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2472 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-29 20:16:34 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	PileupWalker just got a new option: --showIndelPileups. When this option is used, two lines are printed for every genomic location that has indels associated with it: first line is a conventional base pileup, the second line is an "extended event" (indel) pileup. The refence base in that second line is always set to "E" (for Extended), and the pileup string contains I,D,. symbols for insertion, deletion, noevent, respectively. Only this simple short format for indel pileups is implemented so far.	2009-12-29 20:16:34 +00:00
test/org/broadinstitute/sting	Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker	2009-12-29 19:46:29 +00:00