1.7.0

• #254, added the ability to run PepSIRF as a Docker image and added a page for instructions
• #197, resolved CMake not locating OpenMP on MacOS. Tutorial for fix added to installation page.
• #236, added a functionality to the "-i" option in Subjoin to accept a regex pattern instead of a filename which contains sample/peptide names. The sample/peptide names used from the score matrix file will be filtered by whether they contain the regex pattern.
• #234, added "--unmapped-reads-output" option to Demux, which writes all reads that have not been mapped to a sample/peptide to the specified filename.
• #233, changed Deconv "-t" option to accept a tab demilited file with a column for each TaxID and a column for the score threshold to use for that TaxID. The originally functionality still holds: if a number to included with option, each TaxID will use that score threshold.
• #227, Demux outputs additional information about the total number of samples, the number of samples containing a given number of replicates, and the number of samples starting with "Sblk_". The replicate information with be written to the file provided with the option "--replicate_info".
• #223, Added "--exclude" option to subjoin that changes the output data file to contain all of the input samples/peptides except the the ones specified by the user.
• #221, Demux automatically truncates sequences in the library which are longer the than provided length through the "--seq" option. If a sequence is found to be shorter than the specified length, an error is thrown.
• #218, Added "--custom_id_name_map_info" option to Deconv which accepts a filename, the key column header, and the value column header in the file to use to link TaxIDs to taxon names. This option should be used instead of "--id_name_map" if the user wishes to define a tab-delimited ID name map.
• #210, Fixes crash in Link when a species does not have an associated ID. A single warning is logged which informs the user some species have not been considered and where to find a list of those species which should be reviewed.
• #152, Automated tests have been added and finished to test all recently added features and fixed issues in PepSIRF.
• #131, Provides more information in Enrich's failed enrichment output. Sample replicates which do not meet either threshold are identified in the output and are marked as either not meeting the minimum or maximum threshold.
• #56, Alters behavior of Demux when ran in reference independent mode. In ref-independent mode, index toggling is turned off; therefore, if an exact match at the given index is not found, the read is discarded.
• #2, Adds a system to handle logging PepSIRF's progress when running. A default file name is automatically generated with the module name, current time and date. An option '--logfile' which allows the user to provide a custom name for the log file.
• #36, Standardizes the order tied species are listed in Deconv output. If species names are provided, then the tied species are sorted by alphabeticall by their names; otherwise, they are sorted by their species ID.

1.6.0

• #169, Added an option for FASTQ - level outputs to be generated by demux. This is done with the flag "-q" followed by a directory path where files will be generated
• #178, In the case of a sample not having enriched peptides, enrich will now add a space to the empty file. This allows for better compatability with deconv through Qiime2.
• #137, Added an option for enrich to drop replicates with low raw read counts. This is done with the flag "-l" or "--low_raw_reads". If this functionality is invoked, dropped replicates will not be considered in the enrichment process, and the dropped replicates will be reported in the enrichment failure reasons file under "Removed Replicates": each line will contain the replicates removed from a sample.
• #131, Enrich now reports which replicates caused a raw read count threshold failure; and identifies if a replicate failed the maximum or minimum threshold.
• #161, Added a flag to deconv that allows the user to specify what string is expected at the end of each file containing enriched peptides (set to "_enriched.txt" by default). If a file without does not end in the string that was specified, deconv skips over that file.
• #149, Added feature to info that generates a matrix of average counts given replicates. Two new flags must be included in order to use this feature: --rep_names and --get_avgs. --rep_names requires an input file with the names of the replicates that the user wants to generate a matrix of average counts for. --get_avgs requires and output file name where the matrix will be stored.

1.5.1

Re-release of 1.5.1, to trigger archive by Zenodo.

1.5.0

Re-release of 1.5.0, to trigger archive by Zenodo.