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, 21:45, 29 January 2013
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| By default, just the chromosome/position and cigar are compared for each record. | | By default, just the chromosome/position and cigar are compared for each record. |
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| + | Note: The headers are not compared. |
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| Options are available to compare: | | Options are available to compare: |
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| --params : print the parameter settings | | --params : print the parameter settings |
| </pre> | | </pre> |
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| + | == input Files 1 & 2 (<code>--in1</code> and <code>--in2</code>) == |
| + | |
| + | Use <code>--in1</code> and <code>--in2</code> followed by your file names to specify the SAM/BAM input files to compare. |
| + | |
| + | The program automatically determines if your input files are SAM/BAM/uncompressed BAM unless your input file is stdin. |
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| + | A <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM). |
| + | |
| + | {|border="1" cellspacing="0" cellpadding="2" |
| + | |SAM/BAM/Uncompressed BAM from file |
| + | | <code>--in1 yourFileName</code> |
| + | |- |
| + | |SAM from stdin |
| + | | <code>--in1 -</code> |
| + | |- |
| + | |BAM from stdin |
| + | | <code>--in1 -.bam</code> |
| + | |- |
| + | |Uncompressed BAM from stdin |
| + | | <code>--in1 -.ubam</code> |
| + | |} |
| + | |
| + | |
| + | Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported. |
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| = Usage = | | = Usage = |
| ./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params] | | ./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params] |
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| = Return Value = | | = Return Value = |