Make deepTools tolerant towards chromosome naming (chr1 vs. 1) about deeptools HOT 3 CLOSED

#20 should be solved. I tested different options and got the expected results. Anything that is not corrected by adding or removing 'chr' results in a warning message sent to stderr.

I took the chance to modify the behavior of computeMatrix such that by default always outputs warning messages (to stderr). Before only when the --verbose parameter was given such messages were shown. I changed --verbose, for --quiet. I don't know if any changes are required for the galaxy wrappers regarding this change. Also, now I consistently set exit codes equal to 1, when there is an error.

Furthermore, I also change the output of computeMatrix such that now it gives an output that is as close as the original BED file as possible. Regions that are not found on the bigwig file are no longer skipped. Similarly, duplicate regions are not removed be default now but a warning is given in case duplicates are found. This is to allow the user to combine multiple heatmaps by keeping the output consistent.

By accident I added one feature to the profiler tool, which now has the option to input the colors used for the plotted lines.

I wait for green light from Bjoern no merge the 'experimental' branch and close this issue.

from deeptools.

You have my green light 👍

Thanks!

from deeptools.

Merged!

from deeptools.