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.