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Options are available to compare:
Options are available to compare:
* all fields
* flags
* mapping quality
* mate chromosome/position
* insert size
* sequence
* sequence
* base quality
* base quality
* specified tags
* specified tags
* all tags
* turn off position comparison
* turn off position comparison
* turn off cigar comparison
* turn off cigar comparison
Optional Parameters:
Optional Parameters:
--out : output filename, use .bam extension to output in SAM/BAM format instead of diff format.
--out : output filename, use .bam extension to output in SAM/BAM format instead of diff format.
In SAMBAM format there will be 3 output files:
In SAM/BAM format there will be 3 output files:
1) the specified name with record diffs
1) the specified name with record diffs
2) specified name with _only_<in1>.sam/bam with records only in the in1 file
2) specified name with _only_<in1>.sam/bam with records only in the in1 file
3) specified name with _only_<in2>.sam/bam with records only in the in2 file
3) specified name with _only_<in2>.sam/bam with records only in the in2 file
--all : diff all the SAM/BAM fields.
--flag : diff the flags.
--mapQual : diff the mapping qualities.
--mate : diff the mate chrom/pos.
--isize : diff the insert sizes.
--seq : diff the sequence bases.
--seq : diff the sequence bases.
--baseQual : diff the base qualities.
--baseQual : diff the base qualities.
--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--tags : diff the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type...
--everyTag : diff all the Tags
--noCigar : do not diff the the cigars.
--noCigar : do not diff the the cigars.
--noPos : do not diff the positions.
--noPos : do not diff the positions.
= Usage =
= Usage =
./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]
./bam diff --in1 <inputFile> --in2 <inputFile> [--out <outputFile>] [--all] [--flag] [--mapQual] [--mate] [--isize] [--seq] [--baseQual] [--tags <Tag:Type[;Tag:Type]*>] [--everyTag] [--noCigar] [--noPos] [--onlyDiffs] [--recPoolSize <int>] [--posDiff <int>] [--noeof] [--params]
= Return Value =
= Return Value =
The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.
The 3rd line (if a matching record was found) is the flag followed by the diff'd fields from the matching record.
The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:
The diff'd record lines are tab separated, and are in the following order if --onlyDiffs is not specified:
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.
If all fields are diffed and <code>--onlyDiffs</code> is specified, it may be difficult to determine which field is different.
=== Example Output ===
=== Example Output ===
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
* ZF - Flag
* ZF - Flag
* ZP - Pos
* ZP - Chrom/Pos
* ZC - Cigar
* ZC - Cigar
* ZM - Mapping Quality
* ZN - Mate chrom/pos
* ZI - Insert Size
* ZS - Sequence
* ZS - Sequence
* ZQ - Base Quality
* ZQ - Base Quality
* ZT - Tags
* ZT - Tags
