HowToCommit.txt

When ever you modify the repsoitory in any way please include one of the
following as a prefix in your commit message:

[FEATURE, FIX, DOC, INTERNAL, TEST, OTHER]

FEATURE = I added a new feature
FIX = I fixed a bug
DOC = I made changes to the documentation
INTERNAL = I changed something to be more efficient/reliabe/... but it does not change the outcome.
TEST = I added/modified a test.

Please put the tag into square brackets before the short, one sentence message.
If the message is longe please provide a summary message first, add an empty
line and then include the full description of the commit 

For example:
git commit -m "[TEST, FIX] Fixed a bowtie reporting issue and added an appropriate test.

Bowtie2 uses the MAPQ 255 for uniq mappings. According to the BAM specification this number is reserved for: MAPQ not available. Because of this some tools get confused. Therefore I reset a MAPQ of 255 to 60 when using bowtie2."