Provided by: biobambam2_2.0.183+ds-1_amd64 bug

NAME

       bamseqchksum - produce checksums for primary data in BAM files

SYNOPSIS

       bamseqchksum [options]

DESCRIPTION

       bamseqchksum reads a BAM file from stdin, for each record calculates hash digest checksums
       over

       [1]    flags and sequence

       [2]    queryname, flags and sequence

       [3]    flags, sequence and qualities

       [4]    flags, sequence and source data related aux tags

       where the flags are the least significant byte of the BAM FLAGS containing only  the  bits
       for   multiple  segments,  first  segment  and  last  segment.  The  sequence  is  reverse
       complemented, and quality string reversed, before checksumming if the reverse complemented
       bit is set.

       Depending  on the chosen hash digest function either the sum modulo some power of 2 or the
       product modulo a prime number of these checksums is taken over all  non-supplementary  and
       non-secondary   BAM  alignment  records.  Separate  sums  or  products  are  reported  for
       combinations of all and QC pass records and for each readgroup.

       The following key=value pairs can be given:

       verbose=<0>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       inputformat=<bam>: input file format All versions of bamseqchksum come  with  support  for
       the BAM input format. If the program in addition is linked to the io_lib package, then the
       following options are valid:

       bam:   BAM (see http://samtools.sourceforge.net/SAM1.pdf)

       sam:   SAM (see http://samtools.sourceforge.net/SAM1.pdf)

       cram:  CRAM (see http://www.ebi.ac.uk/ena/about/cram_toolkit)

       reference=: file name of the reference for CRAM input files. If this key  is  unset,  then
       the CRAM file header will be scanned for obtaining a reference file name.

       hash=<crc32prod>: hash digest used to compute checksums. All versions of biobambam support
       the following functions:

       crc32prod:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^31-1.  This is the default and only option
              for biobambam versions up to 0.0.174.

       crc32: checksums are computed via crc32 and combined by summing up modulo 2^32.

       md5:   checksums are computed via md5 and combined by summing up modulo 2^128.

       crc32prime32:
              identical with crc32prod (alternate implementation for testing purposes)

       crc32prime64:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^64-59.

       md5prime64:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^64-59.

       crc32prime96:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^96-17.

       md5prime96:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^96-17.

       crc32prime128:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^128-159.

       md5prime128:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^128-159.

       crc32prime160:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^160-47.

       md5prime160:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^160-47.

       crc32prime192:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^192-237.

       md5prime192:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^192-237.

       crc32prime224:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^224-63.

       md5prime224:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^224-63.

       crc32prime256:
              checksums  are  computed  via  crc32  and  combined  over   multiple   records   by
              multiplication modulo the prime number 2^256-189.

       md5prime256:
              checksums are computed via md5 and combined over multiple records by multiplication
              modulo the prime number 2^256-189.

       null:  no checksums are computed and all checksums in the  programs  output  are  0.  This
              option is for performance testing only.

       If libmaus is compiled with support for the nettle library, then the following options are
       available:

       sha1:  checksums are computed via sha1 and combined by summing up modulo 2^160.

       sha1prime64:
              checksums  are  computed  via  sha1  and  combined   over   multiple   records   by
              multiplication modulo the prime number 2^64-59.

       sha1prime96:
              checksums   are   computed   via   sha1  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^96-17.

       sha1prime128:
              checksums  are  computed  via  sha1  and  combined   over   multiple   records   by
              multiplication modulo the prime number 2^128-159.

       sha1prime160:
              checksums   are   computed   via   sha1  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^160-47.

       sha1prime192:
              checksums  are  computed  via  sha1  and  combined   over   multiple   records   by
              multiplication modulo the prime number 2^192-237.

       sha1prime224:
              checksums   are   computed   via   sha1  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^224-63.

       sha1prime256:
              checksums  are  computed  via  sha1  and  combined   over   multiple   records   by
              multiplication modulo the prime number 2^256-189.

       sha224:
              checksums are computed via sha2-224 and combined by summing up modulo 2^224.

       sha224prime64:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^64-59.

       sha224prime96:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^96-17.

       sha224prime128:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^128-159.

       sha224prime160:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^160-47.

       sha224prime192:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^192-237.

       sha224prime224:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^224-63.

       sha224prime256:
              checksums  are  computed  via  sha2-224  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^256-189.

       sha256:
              checksums are computed via sha2-256 and combined by summing up modulo 2^256.

       sha256prime64:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^64-59.

       sha256prime96:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^96-17.

       sha256prime128:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^128-159.

       sha256prime160:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^160-47.

       sha256prime192:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^192-237.

       sha256prime224:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^224-63.

       sha256prime256:
              checksums  are  computed  via  sha2-256  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^256-189.

       sha384:
              checksums are computed via sha2-384 and combined by summing up modulo 2^384.

       sha384prime64:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^64-59.

       sha384prime96:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^96-17.

       sha384prime128:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^128-159.

       sha384prime160:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^160-47.

       sha384prime192:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^192-237.

       sha384prime224:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^224-63.

       sha384prime256:
              checksums  are  computed  via  sha2-384  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^256-189.

       sha512:
              checksums are computed via sha2-512 and combined by summing up modulo 2^512.

       sha512prime64:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^64-59.

       sha512prime96:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^96-17.

       sha512prime128:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^128-159.

       sha512prime160:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^160-47.

       sha512prime192:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^192-237.

       sha512prime224:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^224-63.

       sha512prime256:
              checksums  are  computed  via  sha2-512  and  combined  over  multiple  records  by
              multiplication modulo the prime number 2^256-189.

       sha512primesums:
              checksums  are  computed  via sha2-512 and combined over multiple records by adding
              modulo the Mersenne prime number 2^521-1.

       sha512primesums512:
              checksums are computed via sha2-512 and combined over multiple  records  by  adding
              modulo 2^512-75.

       murmur3:
              checksums        are        computed       via       MurmurHash3_x64_128       (see
              https://github.com/aappleby/smhasher/blob/master/src/MurmurHash3.cpp) and  combined
              over multiple records by summing modulo 2^128.

       murmur3primesums128:
              checksums        are        computed       via       MurmurHash3_x64_128       (see
              https://github.com/aappleby/smhasher/blob/master/src/MurmurHash3.cpp) and  combined
              over multiple records by summing modulo 2^128+51.

AUTHOR

       Written  by David Jackson (using code by German Tischler as a template).  Extended to hash
       digests beyond crc32prod by German Tischler.

REPORTING BUGS

       Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT

       Copyright © 2014-2014 David Jackson, © 2014-2014 Genome  Research  Limited.   Copyright  ©
       2009-2016  German  Tischler, © 2011-2014 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.