0.1.13

• Added the --ignoreFlags/-F option, which is equivalent to the -F option in samtools. The default is 0xF00, which ignores duplicates, QC fail, secondary, and supplemental alignments.

0.1.12

• Fix handling of hard-clipped bases

0.1.11

• Make -d actually work

0.1.10

• Added the --version/-v option.
• Fixed the -h/--help option, which actually wasn't recognized before!
• Added the --minDepth option.
• Fixed handling of the XG auxiliary tag, since some aligners other than bismark are using it (and for different purposes). This is the single biggest annoyance of custom auxiliary tags.

0.1.9: Merge pull request #18 from dpryan79/fix17

• Added the --methylKit option
• Added automated testing with make test