This release re-introduced the option to compute metrics for each gene in an annotation file (GFF). Command-line options relating to this feature have been updated but will not break previous CLI options.

Updated makefile to compile in bioconda testing environment:

• Cleaner specifying of C++ and C compilers
• Removed the CPP variable which was conflicting with the C PreProcessor (CPP) env variable
• Environment variables modifications are appended instead of overwritten

Major update to PSASS. This update modified PSASS's CLI, hence the major version update.

Changelog:

• Implemented a 'pileup' command to generate a sync file from a set of CRAM/BAM files. This command is much faster than samtools mpileup + psass convert and generally speeds up the PSASS pipeline.
• Modified output, now PSASS always outputs a single file containing all sliding window metrics (fst, snps, and depth) and can optionally output the position of pool-specific snps and/or the position of bases with high per-base FST in two separate files. Contig lengths are also included in the window metrics output file, so contig length files are no longer needed to plot results with psass-vis.
• Implemented a cleander command-line interface. Pool names now have to be specified manually, but this means PSASS can be used to compare any two pools, not just "males" and "females".
• Fixed a bug preventing PSASS from correctly computing window metrics at the end of a contig
• Fixed a bug where indels were correctly removed from total depth but still counted in FST computation
• Cleaned up output and log streams (all logs are now output to stderr)
• Cleaned up and improved makefile (thanks @KamilSJaron)

Changelog:

• Implemented a "process" command that converts a pileup file from samtools mpileup into a sync file. This command is faster than popoolation2 mpileup2sync and creates a smaller output file. The format is slightly different from popoolation2, and a new parameter was added to specify the input file's format (--input-format).

• Pool names can now be specified with the parameters --pool1 and --pool2. In the past, the pools were always named "Males" and "Females", this feature adds flexibility. The parameter "--male-pool" was removed accordingly.

• Logs are now output to stderr instead of a log file (logs can be redirected to a file using the bash 2> syntax).

• Fixed a bug where deletions were included in depth computation. After this change, indels are not counted when computing FST between pools.

• The makefile was updated to be more portable.

This version includes a partial rewrite of PSASS with some CLI changes, hence the up in major version number.
Major changes :

• PSASS CLI now has subcommands. The old PSASS is now accessible with the subcommand "analyze"
• FST in a sliding window does not show the number of bases with FST > threshold anymore, but rather the FST between populations for the given window.
• PSASS now output metrics at the beginning and at the end of contigs (for values lower than 1/2 window size). Calculations are performed on whatever bases are covered by the window.

First release of PSASS.
Analyze output of popoolation2 mpileup2sync and output metrics for two pooled-sequencing datasets.