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, 10:17, 19 May 2011
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| * [[C++ Executable: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]] | | * [[C++ Executable: bam#filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]] |
| * [[C++ Executable: bam#readReference|readReference - Print the reference string for the specified region]] | | * [[C++ Executable: bam#readReference|readReference - Print the reference string for the specified region]] |
| + | * [[C++ Executable: bam#diff|diff - Print the diffs between 2 bams]] |
| | | |
| This executable is built using [[StatGenLibrary: BAM]]. | | This executable is built using [[StatGenLibrary: BAM]]. |
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| The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]] | | The <code>filter</code> option on the bam executable filters the reads in a a SAM/BAM file. This option is documented at: [[Bam Executable: Filter]] |
| + | |
| + | == diff == |
| + | <span style="color:#D2691E">'''***Coming Soon***'''</span> |
| + | |
| + | The <code>diff</code> option on the bam executable prints the difference between two SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools. |
| + | |
| + | === Parameters === |
| + | <pre> |
| + | Required Parameters: |
| + | --in1 : first SAM/BAM file to be diffed |
| + | --in2 : second SAM/BAM file to be diffed |
| + | Optional Parameters: |
| + | --seq : diff the sequence bases. |
| + | --baseQual : diff the base qualities. |
| + | --tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type... |
| + | --noCigar : do not diff the the cigars. |
| + | --noPos : do not diff the positions. |
| + | --onlyDiffs : only print the fields that are different, otherwise for any diff all the fields that are compared are printed. |
| + | --recPoolSize : number of records to allow to be stored at a time, default value: 1000000 |
| + | --posDiff : max base pair difference between possibly matching records100000 |
| + | --noeof : do not expect an EOF block on a bam file. |
| + | --params : print the parameter settings |
| + | </pre> |
| + | |
| + | === Usage === |
| + | ./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params] |
| + | |
| + | === Return Value === |
| + | * 0: all records are successfully read and written. |
| + | * non-0: an error occurred processing the parameters or reading one of the files. |
| + | |
| + | === Output Format === |
| + | |
| | | |
| == readReference == | | == readReference == |