bamalignfrac - compute fraction of aligned bases in alignment file

       Written by German Tischler-Höhle.

       Copyright  ©  2009-2019  German  Tischler,  © 2011-2013 Genome Research Limited.  License GPLv3+: GNU GPL
       version 3 <http://gnu.org/licenses/gpl.html>
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to  the  extent
       permitted by law.

BIOBAMBAM                                           July 2019                                    BAMALIGNFRAC(1)

       bamalignfrac  reads  a  SAM/BAM/CRAM  file, computes a set of statistical values and outputs these on the
       standard output channel. The values produced are

       *      the number of names passing a given regex filter

       *      the number of primary alignments

       *      the number of total alignments

       *      the total number of bases

       *      the total number of aligned bases

       *      the fraction of aligned bases

       *      the total number of clipped/unaligned bases

       *      the number of unmapped reads

       These values are printed on the standard output channel at the end of the program run in  the  last  line
       printed by the program. The program prints a set of line description line prior to that.

       The input file needs to be provied in query name sorted order, which can be obtained via e.g.

               $ bamsort SO=queryname

       right before being passed to bamalignfrac.

       The following key=value pairs can be given:

       verbose=<0|1>: print preliminary values for file prefixes while processing the input file

       name=<>: only consider reads matching the given regular expression.  By default all reads are considered.

       bamalignfrac - compute fraction of aligned bases in alignment file

       Report bugs to <germant@miltenyibiotec.de>

bamalignfrac [options] <input.bam>