V0.43.1

Changes from v0.43.0

fusions

kallisto can now find reads which span potential fusion breakpoints. The quant mode adds a --fusion flag which identifies read pairs involved in fusions and writes output to fusion.txt, this file is then processed by pizzly for downstream analysis.

quant mode:

Switched to a uniform point for the EM algorithm that works better in highly ambiguous cases.

pseudobam fixes

Several fixes to the pseudobam output so that the resulting SAM/BAM file can be validated with picard.

Bug fixes

• updates kseq library, which would loop indefinitely on CRC corrupt gzipped files.
• warning when no reads pseudoalign and fixes crash (resulting output file will contain nan for tpm values)