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, 09:57, 21 November 2011
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| Clipping By Coordinate Optional Parameters: | | Clipping By Coordinate Optional Parameters: |
| --poolSize : Maximum number of records the program is allowed to allocate | | --poolSize : Maximum number of records the program is allowed to allocate |
− | for clipping on Coordinate sorted files. (Default: 5000) | + | for clipping on Coordinate sorted files. (Default: 1000000) |
| --poolSkipClip : Skip clipping reads to free of usable records when the | | --poolSkipClip : Skip clipping reads to free of usable records when the |
| poolSize is hit. The default action is to just clip the | | poolSize is hit. The default action is to just clip the |
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| == Set the SAM/BAMs record buffer size (<code>--poolSize</code>) == | | == Set the SAM/BAMs record buffer size (<code>--poolSize</code>) == |
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− | To handle coordinate sorted files, SAM/BAM records are buffered until it is known that all following records will have a later start position. To prevent the program from running away with memory, a limit is set to the number of records that can be buffered (defaults to 5000). | + | To handle coordinate sorted files, SAM/BAM records are buffered until it is known that all following records will have a later start position. To prevent the program from running away with memory, a limit is set to the number of records that can be buffered (defaults to 1000000). |
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| If the poolSize is exhausted, the code will write the earliest record awaiting its overlapping mate and any previous records that are being buffered. | | If the poolSize is exhausted, the code will write the earliest record awaiting its overlapping mate and any previous records that are being buffered. |