pmd-mask v0.3.2

What's Changed

Full Changelog: v0.3.1...v0.3.2

Bugfixes

• Temporary workaround to issue #8 : Providing pmd-mask with an invalid or corrupted fasta index now leads to an uncoverable error.
• Remove debug and memory profiling artifacts (e.g. #[inline(never)]) on some performance critical functions.

API documentation

• Complete genome::Strand documentation + doctests.
• Complete genome::Orientation documentation + doctests.
• Complete genome::coordinate::Position and genome::coordinate::ChrName documentation + doctests.
• Improved logger::Logger documentation
• Complete documentation and doctests for genome::mask::MaskEntry, genome::mask::MaskThreshold and genome::mask::Masks.
• Improved genome::misincorporation::Misincorporations and genome::misincorporation::MisincorporationRecord documentation + doctests.
• Improved parser::Cli and pmd_mask higher-level functions documentation.

pmd-mask v0.3.1

What's changed

• Fixes issue #13 : pmd-mask now correctly handles out of index errors when attempting to retrieve positions that lie beyond the chromosome's length. A ReferenceOutOfIndex error is emmitted if and only if the read happens to not be labeled as 'segment unmapped' (0x4).
• Temporary workaround to issue #15 : The current patch directly uses libc::free to manually clean up memory between each iteration. A more elegant solution may come in the future.
• Use of atty ensures users are actually feeding the program with an input using piping, when they did not use --bam argument. This ensures a comprehensive error message gets printed, instead of letting the program endlessly hanging.
• Improved error handling: