Changes from v0.43.0
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.
Switched to a uniform point for the EM algorithm that works better in highly ambiguous cases.
Several fixes to the pseudobam output so that the resulting SAM/BAM file can be validated with picard.
- 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
nanfor tpm values)