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Jump to navigationJump to search→Overview of the clipOverlap function of bamUtil: add clipping logic
To handle coordinate sorted files, SAM/BAM records are buffered up 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, see [[#Set the SAM/BAMs record buffer size (--poolSize)|<code>--poolSize</code>]] for more information.
To handle coordinate sorted files, SAM/BAM records are buffered up 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, see [[#Set the SAM/BAMs record buffer size (--poolSize)|<code>--poolSize</code>]] for more information.
When two mates overlap, this tool will clip the record's whose clipped region would has the lowest average quality.
It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped.
