cancerit/cgpPindel: Reduces the amount of temporary space required and overall I/O
- Keiran Raine
- David Jones
- jwhsanger
- AndyMenzies
DOIAbstract
To process 40 million readpairs (40x Tumour + 40x Normal, chr21, 100bp reads): Original time: User time (seconds): 3553.88 System time (seconds): 63.92 Percent of CPU this job got: 159% Elapsed (wall clock) time (h:mm:ss or m:ss): 37:51.63 File system inputs: 64 File system outputs: 1782080 New time: User time (seconds): 3572.21 System time (seconds): 74.06 Percent of CPU this job got: 167% Elapsed (wall clock) time (h:mm:ss or m:ss): 36:15.01 File system inputs: 0 File system outputs: 1139128 Original peak size: 650MB New peak size: 291MB ~55% reduction in working space and about 40% fewer writes to the file system. Exactly the same results: $ diff old/f9c3bc8e-dbc4-1ed0-e040-11ac0d4803a9_vs_f9c3bc8e-dbc1-1ed0-e040-11ac0d4803a9.ger...
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