Made it so the genome/protein database builder can read compressed GenBank or JSON files. Added simple scripts to download NCBI refseq viral FASTA or GenBank flat file data.
4.0.16
Not secure
Removed assertion of incorrect assumption that a read CIGAR string cannot start with an insertion, based on a SAM file mapped using Geneious.
4.0.15
Added a simple consensus caller. Still needs to be stress tested in the wild, and will need more tests and code refactoring to make it more broadly useful.
4.0.14
Added internal optimization to make the SAM filtering fast when no filtering is needed (this is the merge of a pull request from July 2021).
4.0.13
Not secure
Added `bin/fasta-count-chars.py` script. Fixed argument bug in `run-bowtie2.py` print statement.
4.0.12
Not secure
Fixed another tiny bug when printing dry run output in `bin/make-consensus.py`.