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 <tischler@mpi-cbg.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.