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.