Salmon 0.14.1 release notes

This is primarily a bugfix release. For the recently-added features and capabilities, please refer to the 0.14.0 release notes.

The following bugs have been fixed in v0.14.1 :

• If the number of skipped CBs are too high, then the reported whitelist can sometimes be from the skipped CB id. Thanks to @Ryan-Zhu for bringing this up and it has been fixed.
• Multiple bugs in --dumpMtx format, thanks to @Ryan-Zhu and @alexvpickering for pointing these out.
  • Expression values can sometimes be reported in scientific notation, which can break certain downstream parsers. This has been modified to fixed-precision decimal (C++ default of a precision of 6).
  • The column ids were 0-indexed while mtx assumes 1-indexing. This has been fixed to report the indices starting from 1.
  • The reported expressions in the mtx file were in column-major format which doesn't align with the binary format counts and the quant_mat_cols.txt. It has been fixed to report row-major order, and now aligns with the order of the genes as reported in quants_mat_cols.txt
• Alevin fails without reporting error when the number of low confidence cellular barcodes are < 1. We have fixed alevin to not perform intelligent whitleisting if the number of low confidence cellular barcodes are <200.

Note : At least one issue has reported a depressed mapping rate with v0.14.1. It is recommended to upgrade to the latest version of salmon.