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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.
Note: The headers are not compared.
Options are available to compare:
Options are available to compare:
--params : print the parameter settings
--params : print the parameter settings
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</pre>
== 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.
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.
= 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]
= Return Value =
= Return Value =
