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test quote reference and chrom name. Jan 30, 2017 bump step size for WGS to reduce hits to index Oct 15, 2016
depth.go update to new gonum layout Sep 12, 2017 fix variable name in test Mar 10, 2017
intervals.go prep for release Sep 10, 2018


depth parallelizes calls to samtools in user-defined windows. It outputs a bed file of callable regions (determined by mincov) and of depth (only windows with <= maxmeandepth are reported.

usage: goleft depth [--windowsize WINDOWSIZE] [--maxmeandepth MAXMEANDEPTH] [--q Q] [--chrom CHROM] [--mincov MINCOV] [--stats] --reference REFERENCE [--processes PROCESSES] [--bed BED] [--prefix PREFIX] BAM

positional arguments:
  bam                    bam for which to calculate depth

  --windowsize WINDOWSIZE, -w WINDOWSIZE
                         window size in which to calculate high-depth regions [default: 250]
                         windows with depth > than this are high-depth. The default reports the depth of all regions.
  --q Q, -Q Q            mapping quality cutoff [default: 1]
  --chrom CHROM, -c CHROM
                         optional chromosome to limit analysis
  --mincov MINCOV        minimum depth considered callable [default: 4]
  --stats, -s            report sequence stats [GC CpG masked] for each window
  --reference REFERENCE, -r REFERENCE
                         path to reference fasta
  --processes PROCESSES, -p PROCESSES
                         number of processors to parallelize.
  --bed BED, -b BED      file of positions or regions. (parallelization will be by region).
  --prefix PREFIX
  --help, -h             display this help and exit