V0.42.2

This is version 0.42.2 of Kallisto.

Updates include

• index
  • the index has been updated to include more of the transcript information
  • indices should be slightly smaller than before
  • indices constructed with previous versions will not work with this version, rerun your index command
• quant
  • Bootstraps can be run in multithreaded mode, use option -t to specify number of threads
  • If only one read of a paired end maps, kallisto will check the transcript positions to discard reads that would go outside of transcript given the mean fragment length.
  • Pseudobam. Pseudoalignments can now be output in SAM format to standard output. For more details on the output see pseudobam
  • Sequence specific bias. kallisto can learn a model for sequence specific bias and correct the abundances accordingly.
  • TSV. All output text files have been changed to .tsv ending.