Man page - bamranksort(1)
Packages contains this manual
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- bamchecksort(1)
- bamfilterflags(1)
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- bamstreamingmarkduplicates(1)
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- normalisefasta(1)
- bamrecompress(1)
- bamcollate2(1)
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- bamcat(1)
- bamsplitdiv(1)
- bam12strip(1)
- bammarkduplicatesopt(1)
- bamauxmerge(1)
- bam12auxmerge(1)
- bamrank(1)
- bamfiltermc(1)
- fastaexplod(1)
- bammaskflags(1)
- bamfeaturecount(1)
- bamclipreinsert(1)
- bamadapterclip(1)
- bamreset(1)
- bamintervalcomment(1)
- bamflagsplit(1)
- bamindex(1)
- bamfilterheader(1)
- bamranksort(1)
- bamtofastq(1)
- bamauxsort(1)
- bamfilterheader2(1)
- bamsort(1)
apt-get install biobambam2
Manual
BAMRANKSORT
NAMESYNOPSIS
DESCRIPTION
AUTHOR
REPORTING BUGS
COPYRIGHT
NAME
bamranksort - sort BAM files by rank
SYNOPSIS
bamranksort [options]
DESCRIPTION
bamranksort reads a BAM file (preferably in nearly sorted order), sorts it in rank order and then outputs a BAM.
The input BAM file must already have the rank prefix added to the alignment names and any attempt to sort a file without these name prefixes will fail. bamranksort also assumes that all alignments of the same name are grouped together (a pair of reads plus any number of supplementary/secondary reads). If it finds any alignments in a separate group the program will exit.
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
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-1: |
zlib/gzip default compression level. |
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0: |
uncompressed. |
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1: |
zlib/gzip level 1 (fast) compression. |
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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
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11: |
igzip compression. |
verbose=<0|1|2>: Valid values are
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0: |
do not print progress report (default). |
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1: |
print progress report to standard error. |
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2: |
print more values for debugging only to standard error. |
md5=<0|1>: md5 checksum creation for output file. This option can only be given if outputformat=bam. Then valid values are
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0: |
do not compute checksum. This is the default. |
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|
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.
misordered=<500000>: number of alignments to accumulate before giving up.
step=<2>: expected increment between ranks.
outputthreads=<[1]>: output helper threads.
AUTHOR
Written by Andrew Whitwham.
REPORTING BUGS
Report bugs to <aw7@sanger.ac.uk>
COPYRIGHT
Copyright ©
2015 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.