- Undid some numba that actually slowed things down
- Change the way iterate_commands works
- Make compare log it's multiprocessing efficiency
- Save all counts into counts_table.npz (thanks https://github.com/apcamargo)
- Avoid sorting pre-sorted BAMs and use multiple threads to index and sort BAMs (thanks https://github.com/apcamargo)
- Handle "--version" in argparse correctly
- Make profile properly handle profile_genes
- Add a "DEPRECATED" flag to standalone profile_genes module
[1.3.0w] - 2020-08-13
- Significant refactoring of controller.py and profile
- Re-writting the test suite to be in multiple modules
- Add numba to filter_reads evaluate_pair method (and a few others; just playing around)
- Optimize compare a bit (load stuff up front)
[1.3.0v] - 2020-08-10
- Change internal structure of test suite
- Delete N_sites and S_sites from gene_info table
- Add "class" to SNVs.tsv
- Add some basic checkpoint logging to Compare
- Add a little bit of documentation to log_utils
- Make "compare" multi-thread in the new way (with spawn)
- Tiny docs change
[1.3.0u] - 2020-08-06
- Add Docker and conda installation instructions to the README
- Edit parse_stb to handle None the same as []
- Add the Docker image and associated files
[1.3.0t / 1.3.0.dev3] - 2020-07-29
- Fix "call_con_snps" to account for cases where there's only a SNP in one sample,
but it's not a consensus SNP
- Make the output of compare generated through SNVprofile (like profile does it)
- Make the SNP table produced by compare actually legable and made in the output
[1.3.0s] - 2020-07-14
- Add "FailureScaffoldHeaderTesting" to readComparer to make sure it can catch exceptions
- Add "high_cov" testing to test over 10,000x coverage
- Fix bug in readComparer when coverage was over 10,000x