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--in2 : second coordinate sorted SAM/BAM file to be diffed
--in2 : second coordinate sorted SAM/BAM file to be diffed
Optional Parameters:
Optional Parameters:
--out : output filename, use .bam extension to output in BAM format instead of diff format.
In BAM format there will be 3 output files:
1) the specified name with record diffs
2) specified name with _only_<in1>.bam with records only in the in1 file
3) specified name with _only_<in2>.bam with records only in the in2 file
--seq : diff the sequence bases.
--seq : diff the sequence bases.
--baseQual : diff the base qualities.
--baseQual : diff the base qualities.
=== Output Format ===
=== Output Format ===
2 Output Formats:
# Diff Format
# BAM Format
==== Diff Format ====
There are 2 types of differences.
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 one file, but not in the other file within the window set by recPoolSize & posDiff
If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.
If <code>onlyDiffs</code> is specified, only the fields that are specified and are different get printed in lines 2 & 3.
==== Example Output ====
===== Example Output =====
Command:
Command:
../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log
../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --seq --baseQual --tags "OP:i;MD:Z" --onlyDiffs --out results/diffOrderSam.log
DEF
DEF
> cd *:0 * * *
> cd *:0 * * *
==== Bam Format ====
use .bam extension to output in BAM format instead of diff format.
In BAM format there will be 3 output files:
# the specified name with record diffs
# specified name with _only_<in1>.bam with records only in the in1 file
# specified name with _only_<in2>.bam with records only in the in2 file
== readReference ==
== readReference ==
