gatk-3.8

History

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
..
java	Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads	2013-03-20 22:54:36 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

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

java

Bugfix for HaplotypeCaller: GSA-822 for trimming softclipped reads

2013-03-20 22:54:36 -04:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00