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, 10:52, 19 May 2011
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| <span style="color:#D2691E">'''***Coming Soon***'''</span> | | <span style="color:#D2691E">'''***Coming Soon***'''</span> |
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− | 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. | + | The <code>diff</code> option on the bam executable prints the difference between two coordinate sorted SAM/BAM files. This can be used to compare the outputs of running a SAM/BAM through different tools/versions of tools. |
| + | |
| + | The <code>diff</code> tool compares records that have the same Read Name and Fragment (from the flag). If a matching ReadName & Fragment is not found, the record is considered to be different. |
| + | |
| + | <code>diff</code> assumes the files are coordinate sorted and uses this assumption for determining how long to store a record before determining that the other file does not contain a matching ReadName/Fragment. If the files are not coordinate sorted, this logic does not work. |
| + | |
| + | By default, just the chromosome/position and cigar are compared for each record. |
| + | |
| + | Options are available to compare: |
| + | * sequence |
| + | * base quality |
| + | * specified tags |
| + | * turn off position comparison |
| + | * turn off cigar comparison |
| | | |
| === Parameters === | | === Parameters === |
| <pre> | | <pre> |
| Required Parameters: | | Required Parameters: |
− | --in1 : first SAM/BAM file to be diffed | + | --in1 : first coordinate sorted SAM/BAM file to be diffed |
− | --in2 : second SAM/BAM file to be diffed | + | --in2 : second coordinate sorted SAM/BAM file to be diffed |
| Optional Parameters: | | Optional Parameters: |
| --seq : diff the sequence bases. | | --seq : diff the sequence bases. |
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| === Output Format === | | === Output Format === |
− | | + | There are 2 types of differences. |
| + | * ReadName/Fragment combo is in one file, but not in the other file within the window set by recPoolSize & posDiff |
| + | * ReadName/Fragment combo is in both files, but at least one of the specified fields to diff is different |
| | | |
| == readReference == | | == readReference == |