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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 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
* 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 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 2nd line is the flag followed by the diff'd fields from one of the records.
If <code>onlyDiffs</code> is specified, only the diff'd fields that are different are printed in lines 2 & 3.
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 fields that are specified and are different get printed in lines 2 & 3.
==== Example Output ====
Command:
../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log
Output:
18:462+29M5I3M:F:295
< a1 1:78
> a1 1:74
1
> a1 1:70 3S1M1S ACGTN ;46>> OP:i:75 MD:Z:30A0C5
2
> a1 1:72 3S1M1S ACGTN ;47>> OP:i:75 MD:Z:30A0C5
ABC
> cd *:0 * * *
DEF
> cd *:0 * * *
== readReference ==
== readReference ==
