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gt1 / biobambam2

Tools for early stage alignment file processing
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bammerge - option for output file not documented #2

Closed keiranmraine closed 8 years ago

keiranmraine commented 9 years ago

bammerge has options to generate md5 and index filenames based on the output file name however this option is not documented in the man page or the -h option.

I've tried various values used in other steps that have this same option (O, outputfile, filename, file).

Having a look at the code I can't see anything that attempts to load any output filenames.

Also the option IL is not in the short help given by -h.

gt1 commented 9 years ago

I have updated the help message to state that one needs to provide values for indexfilename/md5filename to get the respective output files. IL is now in the short help message.