Closed timbitz closed 8 years ago
The SAM fix in 6fce542 should close #9. Though it still doesn't support paired-end SAM output, after that commit Whippet --sam
no longer produces incorrect output, and is samtools silent and compatible.
b6ab3af adds paired-end SAM flags to output. No need for unmapped alignments, as those will always be ignored. #14 still lists circular splicing support, but that will be pushed to a later version, still multimapping reads need support as in #14.
This overwrites the -rc2 release and contains several bugfixes that were still prevalent in some rare cases after the fixes of -rc2. Additionally we have altered all output to the proposed final output format.
Whippet v0.1-rc3 has no backwards compatibility with prior versions..