- Messed with the internals of filter_reads. Moved old methods into deprecated_filter_reads - Changed the options of filter_reads to just do things that it can actually do at the moment - Remove break in "get_paired_reads" when a scaffold isn't in the .bam - Fixed bug in profile_genes resulting from having no SNPs called - Allow changing the options for pairing filters - Allow creation of detailed read report - Allow specification of priority_reads that will not be filtered out
1.2.2
- Have genome_wide report microdiversity if it can - Tried to fix a bug where the "percent_compared" in "inStrain compare" is underreported when run in "genome_wide"
1.2.1
- Fixed typo in spelling of "Reference_SNPs" - Fixed bug reporting refFreq - Add a lot of "fillna(0)"s to the method "genome_wide_si_2" to make the average coverage work out correctly
1.2.0
- Move from 'ANI' in scaffold_profile to "conANI" and "popANI" - Store information on lots more types of SNPs in scaffold_profile - Remove snpsCounted - Make it so profile can handle genes, genome_wide, and figure generation - Make the output of profile a bit more pretty
1.1.3
- Profile genes no longer drops allele_count
1.1.2
- Change genome_wide to include sums of SNPs - GeneProfile now reports reference SNPs as well in terms of N and S - Many updates to plotting function (listed below) - The debug option will now produce a stack track for failed plots - Plot basename now included in figure creation - You can now plot only genomes meeting a breadth requirement - You can now specify which genomes to plot - Fixed bug preventing plots 2 and 7 from being made in a lot of cases - Plot 4 now plots only freq > 0.5 and a set 50 bins