samtools/samtools — pull request #94 by pchines (2013-11-22 19:30:43+00:00)
Title: User-supplied filter flag mask replaces (not just adds to) default mask

This change (and associated test) allows the user-supplied filter-flag mask to override the default mask. Current behavior is to add user-supplied mask bits to the existing mask, which provides no way to reset the default mask.

Allowing users to set this mask explicitly increases the utility of mpileup for certain applications, without additional command line complexity, and without any impact on typical genotyping operation.

This patch requires commit 731d837a4c501cae0dd711c186cef7c31707bff6 be applied to htslib.