partition speed improvement #16
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I could not compile with these changes, the errors were below. I think it is because of flowers9:index_t branch changed index_t to idx_t but in this branch it still uses index_t. Sorry I am not that experienced with git so not sure if there is an elegant way to merge both branches. I manually edit the files in this branch and changed index_t back to idx_t and now it compiles... |
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Dear all, thanks for your interest in MECAT, We have updated MECAT versiong 1.3 and fixed these issues by adding one new option '-k to specified the number of partition files. Please complie the new version again and use '-k -1' to let mecat2cns write as many as possible partition files at one pass. Thanks. |
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When partitioning the *.can file, multiple passes are required - one per 10 output files (plus one to get the number of reads involved). As the *.can file can be many gigabytes, this slows down the partitioning process quite a bit. This fix increases the number of files that can be written to be closer to the system limit, rather than a fixed 10, likely reducing the number of passes to one (plus the one to get the number of reads).
My initial approach of using std::vector<PODArray > failed when other variables got overwritten. I didn't want to muck around in PODArray<> to figure out what the cause was, so I used new[]/delete[] instead.