SAMstats

Scripts that implement samtools flagstat functionality, but provide statistics for individual reads rather than individual alignments

small example file

Script can be run in multi-threaded mode (actually turns out slower due to thread lock) or in non-threaded mode:

multithreaded version:

SAMstatsParallel \
  --sorted_sam_file examples/wgs_bam_NA12878_20k_b37_NA12878.sam \
  --outf stats.parallel.txt \
  --chunk_size 1000  \
  --threads 2

singlethreaded version:

SAMstats \
  --sorted_sam_file examples/wgs_bam_NA12878_20k_b37_NA12878.sam \
  --outf stats.txt \
  --chunk_size 1000 

Benchmarks

https://docs.google.com/presentation/d/1QyyDMHlYEJdyl-1rH6Z_YoqwT41zsB9MdH-LXjMM8pw/edit#slide=id.g5c152d9ebd_0_40