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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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Release v0.1-rc3 #13

Closed timbitz closed 8 years ago

timbitz commented 8 years ago

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..

timbitz commented 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.

timbitz commented 8 years ago

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.