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| <pre> | | <pre> |
| Required Parameters: | | Required Parameters: |
− | --in : the SAM/BAM file to be read
| + | --in : the SAM/BAM file to be read |
− | --out : the SAM/BAM file to be written
| + | --out : the SAM/BAM file to be written |
| Optional Parameters: | | Optional Parameters: |
− | --noeof : do not expect an EOF block on a bam file.
| + | --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 === |
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| <pre> | | <pre> |
| Required Parameters: | | Required Parameters: |
− | --in : the SAM/BAM file to be split
| + | --in : the BAM file to be split |
− | --out : the base filename for the SAM/BAM files to write into. Does not include the extension.
| + | --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.
| + | _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.
| + | --noeof : do not expect an EOF block on a bam file. |
− | --bamIndex : the path/name of the bam index file
| + | --bamIndex : the path/name of the bam index file |
− | (if not specified, uses the --in value + ".bai")
| + | (if not specified, uses the --in value + ".bai") |
− | --bamout : write the output files in BAM format (default).
| + | --bamout : write the output files in BAM format (default). |
− | --samout : write the output files in SAM format.
| + | --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] |
| | | |
| | | |
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the BAM file to be read
| + | --in : the BAM file to be read |
− | --out : the SAM/BAM file to write to
| + | --out : the SAM/BAM file to write to |
− | Optional Parameters:
| + | Optional Parameters: |
− | --noeof : do not expect an EOF block on a bam file.
| + | --noeof : do not expect an EOF block on a bam file. |
− | --bamIndex : the path/name of the bam index file
| + | --bamIndex : the path/name of the bam index file |
− | (if not specified, uses the --in value + ".bai")
| + | (if not specified, uses the --in value + ".bai") |
− | --refName : the BAM reference Name to read (either this or refID can be specified)
| + | --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)
| + | --refID : the BAM reference ID to read (defaults to -1: unmapped) |
− | --start : the 0-based start position (defaults to -1)
| + | --start : inclusive 0-based start position (defaults to -1) |
− | --end : the 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) |
| + | --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 === |
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --in : the SAM/BAM file to be read
| + | --in : the SAM/BAM file to be read |
− | Optional Parameters:
| + | Optional Parameters: |
− | --noeof : do not expect an EOF block on a bam file.
| + | --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).
| + | --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 === |
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| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
− | Required Parameters:
| + | Required Parameters: |
− | --bamIndex : the path/name of the bam index file to display
| + | --bamIndex : the path/name of the bam index file to display |
− | Optional Parameters:
| + | Optional Parameters: |
− | --refID : the reference ID to read, defaults to print all
| + | --refID : the reference ID to read, defaults to print all |
− | --summary : only print a summary - 1 line per reference.
| + | --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 === |
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| 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 === |