Streaming Bam Stats utility based on Bamtools Stats
It reads a bamfile given on the commandline, or if none is given the stdin, and output statistics per a given amount of read processed. The default update rate is 100 reads, but can be changed with the -u parameter
bamstatsalive [options] [bam-file]
Options:
-u updateRate [default=100] The number of reads bamstatsalive needs to process before producing another statistics update
-f firstUpdateRate [default=0] The number of reads bamstatsalive needs to process before producing the first statistics update. Useful to increase app responsiveness
-r regionJson A json string describing the sampled regions, needed for coverage histogram. Format: {["chr":"1", "start": 100, "end": 200}, ...]}
-k coverageSkipFactor [default=10] Only 1 in every skipFactor region is used to update coverage histogram, for performance reason.
If no bam-file is specified, input is then read from stdin