NAME

       bamintervalcomment - sort BAM files by coordinate or query name

SYNOPSIS

       bamintervalcomment [options]

DESCRIPTION

       bamintervalcomment  reads  a  BAM,  SAM or CRAM file and a file containing a list of named
       intervals, marks each line in the input with the list of all matching intervals and stores
       the resulting file in BAM, SAM or CRAM format.  The intervals file needs to be given using
       the intervals key. The file can be either plain or compressed using  gzip.  The  intervals
       file  is  expected to contain one interval per line. Each line is assumed to contain a tab
       separated list of values, where the following columns are used by the program:

       first and second column
              contain a pair of names which form the id of the interval

       third column
              gives the name of the reference sequence containing the interval

       fifth and sixth column
              give the interval on the reference sequence designated by the  third  column  as  a
              pair of non negative integers. Both borders are included.

       For  each  alignment  the  matching  interval  designators  are stored in the CO (comment)
       auxiliary field in the form of a semicolon separated list, where each list  element  is  a
       pair (A,B) given the two id columns of the respective interval.  An example of an interval
       file                  can                  be                   found                   at
       http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz .

       The following key=value pairs can be given when running the program:

       level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     zlib/gzip level 9 (best) compression

       If  libmaus  has  been compiled with support for igzip (see https://software.intel.com/en-
       us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-
       data) then an additional valid value is

       11:    igzip compression

       verbose=<1>: Valid values are

       1:     print progress report on standard error

       0:     do not print progress report

       tmpfile=<filename>: set the prefix for temporary file names

       disablevalidation=<0|1>: sets whether input validation is performed. Valid values are

       0:     validation is enabled (default)

       1:     validation is disabled

       md5=<0|1>:  md5  checksum  creation  for  output  file.  This  option can only be given if
       outputformat=bam. Then valid values are

       0:     do not compute checksum. This is the default.

       1:     compute checksum. If the md5filename key is set, then the checksum  is  written  to
              the given file. If md5filename is unset, then no checksum will be computed.

       md5filename file name for md5 checksum if md5=1.

       index=<0|1>:  compute  BAM  index  for  output  file.  This  option  can  only be given if
       outputformat=bam. Then valid values are

       0:     do not compute BAM index. This is the default.

       1:     compute BAM index. If the indexfilename key is set, then the BAM index  is  written
              to the given file. If indexfilename is unset, then no BAM index will be computed.

       indexfilename file name for output BAM index if index=1.

       inputformat=<bam>:  input  file  format.   All  versions  of  bamintervalcomment 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)

       outputformat=<bam>:  output  file  format.   All  versions of bamintervalcomment come with
       support for the BAM output 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).   This  format  is  not
              advisable for data sorted by query name.

       I=<[stdin]>: input filename, standard input if unset.

       O=<[stdout]>: output filename, standard output if unset.

       inputthreads=<[1]>: input helper threads, only valid for inputformat=bam.

       outputthreads=<[1]>: output helper threads, only valid for outputformat=bam.

       reference=<[]>: reference FastA file for inputformat=cram and outputformat=cram. An  index
       file (.fai) is required.

       range=<>:  input  range  to  be  processed.  This  option  is only valid if the input is a
       coordinate sorted and indexed BAM file

       intervals=<>: file name of intervals file

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT

       Copyright © 2009-2014 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.