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, 13:15, 19 May 2011
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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. |
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− | 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. |
| | | |
− | If <code>onlyDiffs</code> is NOT specified, all the fields that are diff'd (per the parameter settings) are 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 |
| | | |
− | The diff'd lines are tab separated:
| + | 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 == |