Initial parsing script from which the tool grew
Initial tool, grown from bam-coverage.py
Version 2
Version 3
Version 4. This added a command line interface via optparse.
Version 5. Changed it to ignore all variants that are not ACGT SNVs, at the point of VCF parsing.
Version 6. Can read from stdin, handle case where there is no major allele (when the only one above the threshold is not a simple ACGT SNV)
Version 7. Fixes, changing command line interface, making header line more easily customizable
Added Galaxy tool xml file
Adding ability to report by strand. Added -s flag to interface, wrote new get_read_counts(), but not tested yet.
Reworked get_read_counts() and get_read_counts_filt() (now process_read_counts()) to make the latter use the former, simplify code, and make ordering optional.
Refactored get_read_counts() and process_read_counts() again to make the output of the former the input of the latter.
This is more natural, since the former gathers the data and the latter refines it.
Still failing some tests (regressions vs. old version)
Added test datasets to version control
Renamed test files, updated real.csv.out to be consistent with current version.
Modified gathering of read counts and encoding in output columns to accommodate stranded and unstranded outputs
Added automated testing script
Refined test script. Now can be called from any cwd.
More testing tools. Reworked debug mode in allele-counts.py, added ability to restrict by sample, added compute-site.py for quick, straightforward computing of site stats.
Fixed error in compute-site.py's computing of allele frequency in getting strand bias.
Added test datasets: real chrM, first stranded test