Mark DePristo 53a904bcbd Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads ... -- Previous version would not trim down soft clip bases that extend beyond the active region, causing the assembly graph to go haywire. The new code explicitly reverts soft clips to M bases with the ever useful ReadClipper, and then trims. Note this isn't a 100% fix for the issue, as it's possible that the newly unclipped bases might in reality extend beyond the active region, should their true alignment include a deletion in the reference. Needs to be fixed. JIRA added -- See https://jira.broadinstitute.org/browse/GSA-822 -- #resolve #fix GSA-822		2013-03-20 22:54:36 -04:00
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src/org/broadinstitute/sting	Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads	2013-03-20 22:54:36 -04:00
test/org/broadinstitute/sting	Merge pull request #120 from broadinstitute/aw_reduce_reads_clear_name_cache	2013-03-20 19:47:42 -07:00