Fixing the bug of the rl parameter in command line.
Comment/date fixes
Fix in version and update information.
Fixes in handling of absent quality values when using -use_qual
Changed line endings to UNIX
Changed bowtie2 command to include -x, which is...
Implemented custom -align_threshold (equal to 0...
Fixed crash when there was no final contigs fil...
Fixed problem with final contig check. Provisory.
Changed -aux_starter routines to use the intern...
Fixed duplicated word in log file message.
Commented out commands for detailed stack trace.
Improved error handling and messages to the scr...
Added message with number of reads converted fr...
Changed ABySS executable name to ABYSS instead ...
Fix in assembler name checking.
Changed parameter -next_seed_size to -ext_seed_...
Die on bad command-line option; Fixed unclosed ...
Fixes in temp file or dir deletion, and use of ...
Fixes in handling of quality use parameter
Initial commit of GenSeed-HMM