gatk-3.8

History

Eric Banks 9c0207f8ef Fixing BQSR/BAQ bug: If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases). The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated. Added a unit test to ensure that the tags are removed in such a case.	2013-01-31 11:03:17 -05:00
..
BAQUnitTest.java	Fixing BQSR/BAQ bug:	2013-01-31 11:03:17 -05:00

Eric Banks 9c0207f8ef Fixing BQSR/BAQ bug:

If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would
fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases).
The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated.
Added a unit test to ensure that the tags are removed in such a case.

2013-01-31 11:03:17 -05:00

BAQUnitTest.java

Fixing BQSR/BAQ bug:

2013-01-31 11:03:17 -05:00