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1,078 bytes added
, 16:51, 18 November 2011
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| Returns the SamStatus for the reads/writes. | | Returns the SamStatus for the reads/writes. |
| + | |
| + | Returns SamStatus::NO_MORE_RECS, 2, if it was clipping files sorted by coordinate and it ran out of records in the pool so had to clip based on the <code>--poolSkipClip</code> setting. |
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| = Output = | | = Output = |
| | | |
− | The number of records that are expected to overlap with a mate (based on the mate information), but could not be matched up with the mate (based on mate positions & read names) is printed to stderr after the run has completed.
| + | All status messages are written to stderr. |
| + | |
| + | {|border="1" cellspacing="0" cellpadding="2" |
| + | ! Situation !! Sorted Type !! Output Message |
| + | |- |
| + | | Everything ran successfully |
| + | | ReadName/Coordinate |
| + | | |
| + | Completed ClipOverlap Successfully. |
| + | |- |
| + | | Failed to allocate any records |
| + | | ReadName/Coordinate |
| + | | |
| + | Failed to allocate any records. |
| + | Failed to complete ClipOverlap. |
| + | |- |
| + | | Error writing a record |
| + | | ReadName |
| + | | |
| + | Failed to complete ClipOverlap. |
| + | |- |
| + | | Expected pair to overlap, but 2nd read was not found in the specified position (may be combined with output for running out of pooled records) |
| + | | Coordinate |
| + | | |
| + | Failed to find expected overlapping mates for XX records. |
| + | Completed ClipOverlap Successfully. |
| + | |- |
| + | | Ran out of pooled Records with <code>--poolSkipClip</code> setting |
| + | | Coordinate |
| + | | |
| + | Due to hitting the max record poolSize, had to skip clipping XX records. |
| + | Completed ClipOverlap. |
| + | |- |
| + | | Ran out of pooled Records without <code>--poolSkipClip</code> setting |
| + | | Coordinate |
| + | | |
| + | Due to hitting the max record poolSize, had to default clip XX records. |
| + | Completed ClipOverlap. |
| + | |- |
| + | | Any other error |
| + | | Coordinate |
| + | | |
| + | Failed to complete ClipOverlap. |
| + | |} |
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− | When processing has been completed, "Completed ClipOverlap." is printed to stderr.
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| <pre> | | <pre> |
| Failed to find expected overlapping mates for 2 records. | | Failed to find expected overlapping mates for 2 records. |
| + | Due to hitting the max record poolSize, had to default clip 9 records. |
| Completed ClipOverlap. | | Completed ClipOverlap. |
| </pre> | | </pre> |