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<span style="color:#D2691E">'''***Coming Soon***'''</span>
<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.
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.
=== 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 ==
