separate directories, add an align-to-ref bam
break out "all" to a base Snakefile [ci skip]
increase memory for blastn, change ref genome
figure out ref name automatically instead of having to specify it [ci skip]
fix up run-pipes.sh to read important paths from config.json [ci skip]
fix fasta indexing in assembly [ci skip]
fix bash line [ci skip]
begin work on tree building and snp calling [ci skip]
more clean up of consolidate reports [ci skip]
convert gzip.GzipFile calls to gzip.open, which plays much nicer with strings and text
sometimes bsub has trouble talking to scheduler
modify rachels calls_snps_3 code to be py2.7 friendly
rework read_utils.split_reads to use numeric file indexes and work on gzipped inputs and outputs
update usage text [ci skip]
reblock select_reads to close file handles more regularly and allow for gzipped i/o. add a deplete_blastn_paired which calls deplete_blastn twice as well as read_utils.purge_unmated twice as a speed optimization
rework hs_deplete pipeline to split samples into 5 chunks to speed up the large read sets
toolify picard and samtools further, add a bunch of picard and samtools entry points, convert snakemake pipelines to use those new entry points, move mvicuna rmdup to read_utils from taxon_filter, convert a bunch of os.system to subprocess.check_call
fix string parsing for version number
make generic picard entry point, make picard default mem specific to the command, clean up tmpfiles in tests
implement read splitting in bam, add a revert step early on in hs_deplete, and rework splitting in hs_deplete