NAME

       lasToBAM - convert daligner las to sam/bam/cram

SYNOPSIS

       lasToBAM [options]

DESCRIPTION

       lasToBAM reads one or two dazzler DB files and a daligner las file and produces a sam, bam
       or cram file of the contained alignments. A FastA file corresponding to the first  of  the
       two dazzler databases must be given via the reference key. In addition a FastA index (.fai
       file) needs to be present for this FastA file. Such an  index  can  be  generated  by  the
       normalisefasta program of biobambam2 or using samtools faidx. The FastA file needs to have
       the sequences of the first dazzler database in the same  order,  but  can  have  different
       names,  which  may  be  convenient as the dazzler database expects a certain naming scheme
       while the desired reference may have other names.

       The following key=value pairs can be given:

       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

       supstrat=<[none]>: query string storage strategy for supplementary reads  (soft,  hard  or
       none, default: none)

       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.

       outputformat=<bam>: output file format.  All versions of bamsort 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.

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

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

       reference=<[]>: reference FastA file

       calmdnm=<0|1>: calculate the MD, NM and AS fields

       threads=<>: number of threads used for conversion. By default this is chosen as the number
       of CPU cores detected on the machine.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

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

COPYRIGHT

       Copyright   ©   2009-2015   German   Tischler.    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.