README

To build:
	cd src
	type make

Documentation:

	Usage:   samstat <file.sam> <file.bam> <file.fa> <file.fq> .... 
	Options:
		-s             STR    prints summary statistics of multiple libraries into one FILE [NA].
		-k             INT    treat all reads mapping more than k errors as unmapped [off].
		-n             STR    name of library and output file when reading from stdin
		-f             STR    specifies the format when reading from stdin.
		-F             INT    filter used in samtools [768].

	Example: Reading from standard input:

	cat library.sam | samstat -f sam -n library_one
	or:
	samtools view -ub  ~/tmp/small.bam   | ./samstat -f bam -n library_one

	In both cases SAMStat will list the stats in the file "library_one.html"

Contact:

Timo Lassmann <timolassmann@gmail.com>