Skip to content

Salmon 0.7.2
Compare
Choose a tag to compare
@rob-p rob-p released this 31 Aug 23:10
· 1591 commits to master since this release
v0.7.2
549fd7e

Bug Fixes

  • Removed attempt to copy un-necessary file (related to EMPH, the old perfect hash function) in fetchRapMap.sh
  • Fixed default alignment-mode options to be consistent with mapping-mode
    • Default maximum fragment length increased from 800 to 1000
    • Default alignment-mode auxiliary directory is now named aux_info as in mapping-mode
  • Fixed description of library types in lib_format_counts.json
    • Fixed string representation of single-end stranded reads (SF and SR rather than F & R as before)
    • Fixed duplicate entires in lib_format_counts.json
  • Fixed various other typos in the --help menus, including the removal of a duplicate option in alignment-based mode

Minor changes & improvements

  • Bumped to the latest version of spdlog.
  • Bumped to the latest version of Staden IO
  • The automatically detected library type is now applied slightly earlier, so that fewer fragments that map inconsistently with which is eventually considered to be the library format will be considered.
  • meta_info.json now contains information about the number of posterior samples, regardless of whether these were obtained with bootstrapping or posterior Gibbs sampling.

New features

  • Added the ability to write out mapping information to SAM format — When Salmon is run in mapping mode (with the quasi index), you can now have it write out information about the quasi-mappings it uses for quantification. This behavior is enabled with the option --writeMappings. If this option is provided with no arguments, it will, by default, write the mapping information to stdout (this can then be piped to e.g. samtools and converted to BAM format). Optionally, you may also provide this argument with a filename, in which case the mapping information will be written to that file in SAM format.
    • Note: In the 0.7.2 release, the file provided to --writeMappings must use a qualified path (e.g. --writeMappings=./out.sam rather than --writeMappings=out.sam), this constraint is already addressed on develop and will be fixed in the next release. Further, note that, because --writeMappings has an implicit argument (stdout), any explicit argument must be directly adjacent to the option; i.e. --writeMappings=./out.sam is OK, but --writeMappings ./out.sam is not — this is a fundamental limitation of how boost program_options handles implicit values.
    • Note: The mapping information is computed and written before library type compatibility checks take place, thus the mapping file will contain information about all mappings of the reads considered by Salmon, even those that may later be filtered out due to incompatibility with the library type.
  • Added the ability to perform automatic library type detection in alignment-based mode.
    • Note: The implementation of this feature involves opening the BAM file, peaking at the first record, and then closing it to determine if the library should be treated as single-end or paired-end. Thus, in alignment-based mode automatic library type detection will not work with an input stream. If your input is a regular file, everything should work as expected; otherwise, you should provide the library type explicitly in alignment-based mode.
    • Note: The automatic library type detection is performed on the basis of the alignments in the file. Thus, for example, if the upstream aligner has been told to perform strand-aware mapping (i.e. to ignore potential alignments that don't map in the expected manner), but the actual library is unstranded, automatic library type detection cannot detect this. It will attempt to detect the library type that is most consistent with the alignment that are provided.

Thanks

This release contains fixes to bugs reported by (or features suggested by) the following people:

Assets 4
Loading