Samtools macos homebrew9/26/2023 duplicate-remover statistics tracking now functions properly: previously the good_bases_out value was not correct when using the sequence info option.merge-methcounts now only counts non-mutated site information and doesn’t break while parsing mutated contexts. The mutation tracking in methcounts introduced a bug in merge-methcounts when parsing mutated contexts.Fixed bug in bsrate causing abort while processing reads that hang over the end of a chromosome (and added warning message).Fixed bug in methcounts caused by improperly checking for write-privileges before opening output file stream.Compressed source generated from github did not contain submodule smithlab_cpp, rendering it uncompilable from the website.The whole package is now based on C++11, allowing future enhancements.The manual is updated with the information of the new WGBS mapper `walt`. All downstream programs are compatible with the header now. The `methcounts` format now allows user-specified header lines, starting with “#”, to provide more information.Fixed a bug in the `dmr` program, which used to report fewer DMR regions than it should be.This version requires that the smithlab_cpp library is built separately (likely will be changed in future release).Code now links to HTSlib for any BAM/SAM format I/O (optional).Major feature added: capacity to read gzip format in many tools.Fixes a problem with the MappedRead class that was crashing programs that used them.bsrate, duplicate-remover, methcounts and methstates now use the formatted SAM files as input.SAM files generated by other mappers can similarly be provided as input, but the mapper of origin must be specified with the -f flag (currently supported mappers are abismal, bismark and bsmap) This tool converts paired-end reads to single-end by merging mates, and also formats the single-end mapped reads to a standardized format used by downstream tools. to-mr is replaced by format_reads, and must be run both on abismal outputs and in SAM files generated by other mappers.we recommend mapping reads using the new abismal software tool, which generates SAM output.HTSLib is used for BAM file decompression, so BAM and SAM files can be used interchangeably. Installation of the htslib can be done through apt, brew or by following the installation guidelines.
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