NAME

       bamalignfrac - compute fraction of aligned bases in alignment file

SYNOPSIS

       bamalignfrac [options] <input.bam>

DESCRIPTION

       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.

AUTHOR

       Written by German Tischler-Höhle.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       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.