Bowtie Code

Updated Ensembl version in jar names in sidebar

Update to reflect recent fixes

Second attempt to fix spurious /1 / /2 at end of label names

Trying to fix issue where /1 / /2 start appearing in labels between align and overlap steps

Another (final?) attempt to fix the mkpath issue.

Fixing my incorrect solution to the mkpath problem. verbose => 0 actually enables verbose mode. The problem was with the two occurrences where mkpath was called with a list argument. Those have been replaced with scalar-arg calls.

For good measure, now specifying { verbose => 0 } in all cases where mkpath is called. In an experiment I ran recently, mkpath seemed to spuriously print the mkdir command to stdout, messing up the pipeline.

Trying to fix issue with spurious "mkdir" output

Final 1.2.0 tweaks

Final changes before 1.2.0