Release v1.3.0 [2020/06/17]

Features

• Faster and more efficient index creation (libdivsufsort), requires about 6n main memory (for fasta files >2GB about 10n main memory). n is the size of the input fasta files. No additional secondary memory is needed (unlike for Skew)
• slightly smaller indices (about 0.625n - 0.75n less space). Old indices are still compatible with GenMap 1.3.0, but indices built with 1.3.0 are not compatible with older versions of GenMap.

Fixes

• indexing will search for fasta files recursively (subfolders were not considered before)
• updated paper information (replaced bioRxiv with OUP Bioinformatics)

Release v1.2.0 [2020/02/21]

Features

• BREAKING CHANGE! k-mers are searched on both strands by default. Can be turned off with --no-reverse-complement
• bedgraph output (*.bg) replaces bed output (*.bed) (bed output is still supported with --bed but deprecated and removed from the help string)
• allow user to specify a filename with --output if only a single fasta file has been indexed (previously only the directory could be specified)

Fixes

• truncate fasta identifiers after first space
• allow indexing fasta files with *.fas filename ending
• runtime speedup when BED file is provided for computation on a subset of the input (--selection)
• reduced progress output on terminal when processing multiple fasta files

Release v1.1.0 [2019/11/17]

Major release 1.1.0

• compute mappability of selected regions using a bed file (-S /path/to/file.bed)
• suppress 0 values in BED and WIG files
• change default algorithm for indexing to Skew

Release v1.0.2 [2019/09/04]

Minor release 1.0.2

• BED output format fixed (end position was off by one, i.e., closed interval instead of half-closed interval)

Release v1.0.1 [2019/06/11]

Minor release 1.0.1

• --frequency-small would output unreadable ascii characters in --txt format
• some typo fixes

Release v1.0 [2019/05/27]

This is the first major release of GenMap.

Changes to the pre-release version (0.9):

• slightly faster computation of mappability for 3 and 4 errors
• included the reference to the paper (preprint)
• minor fixes in documentation and error messages