broadinstitute/picard — pull request #17 by marcelm (2014-06-02 10:42:25+00:00)
Title: Clarify what a "non-PF read" is.

I've been having trouble finding an explanation for what the `INCLUDE_NON_PF_READS` option achieves. All hits on Google lead back to Picard, but the Picard docs never explain what `PF` means. This commit attempts to fix this, at least for SamToFastq.