3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
<pre>
<pre>
Required Parameters:
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--noeof]
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--noeof] [--params]
=== Return Value ===
=== Return Value ===
<pre>
<pre>
Required Parameters:
Required Parameters:
--in : the BAM file to be split
--out : the base filename for the SAM/BAM files to write into. Does not include the extension.
_N will be appended to the basename where N indicates the Chromosome.
Optional Parameters:
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout]
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--noeof] [--bamout|--samout] [--params]
=== Parameters ===
=== Parameters ===
<pre>
<pre>
Required Parameters:
--in : the BAM file to be read
--out : the SAM/BAM file to write to
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--refName : the BAM reference Name to read (either this or refID can be specified)
--refID : the BAM reference ID to read (defaults to -1: unmapped)
--start : inclusive 0-based start position (defaults to -1)
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>]
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--noeof] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--params]
=== Return Value ===
=== Return Value ===
=== Parameters ===
=== Parameters ===
<pre>
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--printRecordRefs : print the reference information for the records in the file (grouped by reference).
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs]
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
=== Return Value ===
=== Return Value ===
=== Parameters ===
=== Parameters ===
<pre>
<pre>
Required Parameters:
--bamIndex : the path/name of the bam index file to display
Optional Parameters:
--refID : the reference ID to read, defaults to print all
--summary : only print a summary - 1 line per reference.
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary]
./bam dumpIndex --bamIndex <bamIndexFile> [--refID <ref#>] [--summary] [--params]
=== Return Value ===
=== Return Value ===
Required Parameters:
Required Parameters:
--refFile : the reference
--refFile : the reference
--refName : the BAM reference Name to read (either this or refID can be specified)
--refName : the SAM/BAM reference Name to read
--start : inclusive 0-based start position (defaults to -1)
--start : inclusive 0-based start position (defaults to -1)
Required Length Parameter (one but not both needs to be specified):
Required Length Parameter (one but not both needs to be specified):
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--end : exclusive 0-based end position (defaults to -1: meaning til the end of the reference)
--numBases : number of bases from start to display
--numBases : number of bases from start to display
--params : print the parameter settings
</pre>
</pre>
=== Usage ===
=== Usage ===
./bam readReference --refFile <referenceFilename> --refName <reference Name>--start <0 based start> --end <0 based end>|--numBases <number of bases>
./bam readReference --refFile <referenceFilename> --refName <reference Name> --start <0 based start> --end <0 based end>|--numBases <number of bases> [--params]
=== Return Value ===
=== Return Value ===
