Instrain

- Apply a mutliprocessing patch to help python version 3.6
- Allow the Docker to accept a FOF for inStrain compare input
- Have the Docker download a reduced IS profile for running compare**

- Backwards compatibility when running inStrain compare on old inStrain profiles
- Print some more info before crashing due to no scaffolds detected
- Update the Docker to be able to handle compare

- More updates to the docs
- Bugfix regarding .stb files when scaffolds are present in the .fasta file, but not the .bam file

- More upgrades to the docs
- An additional refinement to creating profile_merge jobs in linear time even when the amount of genes loaded is huge

- Fixed a bug in quick_profile where it didn't work without an .stb file
- Optimize gene initilization
- Put the split merging + gene profiling in groups
- Add logging of how long groups take to run
- Edited the Docker image to work with version 1.3
- Overhaul of the Glossary
- Update the Docker

- 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