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1,005 bytes added, 12:15, 19 May 2011
* 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
Each difference output consists of 2 or 3 lines. If the record only appears in one of the files, the diff is 2 lines, if it appears in both files, the diff is 3 lines.
The first line of the difference output is just the read name.
The 2nd and 3rd line (if present) begin with either a '<' or a '>'. If the record is from the first file (--in1), it begins with a '<'. If the record is from the 2nd file (--in2), it begins with a '>'.
The 2nd line is the flag followed by the diff'd fields from one of the records.
The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:* '<' or '>'* flag* chrom:pos (chromosome name ':' 1 based position) - if --noPos is not specified* cigar - if --noCigar is not specified* sequence - if --seq is specified* base quality - if --baseQual is specified* tag:type:value - for each tag:type specified in --tags* ...* tag:type:value If <code>onlyDiffs</code> is specified, only the diff'd fields that are specified and are different are get printed in lines 2 & 3.
If <code>==== Example Output ====Command: ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs<--out results/code> is NOT specified, all the fields that are diff'd (per the parameter settings) are printed in lines 2 & 3diffOrderSam.log
The diff'd lines are tab separatedOutput:18:462+29M5I3M:F:295< a1 1:78> a1 1:741> a1 1:70 3S1M1S ACGTN ;46>> OP:i:75 MD:Z:30A0C52> a1 1:72 3S1M1S ACGTN ;47>> OP:i:75 MD:Z:30A0C5ABC> cd *:0 * * *DEF> cd *:0 * * *
== readReference ==

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