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* 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.
== readReference ==
