Created
August 2, 2011 09:00
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wavelet tree profiling
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| // Test case: ~600 Mbp of 150bp E. coli sequence reads | |
| // | |
| // SGA FM-index | |
| // | |
| Symbols: 605264456 Bytes: 121737401 (0.20 bytes per symbol) | |
| Calculated 100000000 occurrence values in 21.28 seconds (0.212800 us/call) | |
| // | |
| // WaveletTree with MapperCont, wt_coder_huff, BSB_RG | |
| // | |
| Encoded 605264456 symbols in 178896488 bytes -- 3.38 symbols per byte, 0.30 bytes per symbol | |
| Calculated 100000000 rank values in 75.18 seconds (0.751800 us/call) | |
| // | |
| // WaveletTree with MapperCont, wt_coder_huff, BSB_RRR | |
| // | |
| Encoded 605264456 symbols in 86904920 bytes -- 6.96 symbols per byte, 0.14 bytes per symbol | |
| Calculated 100000000 rank values in 166.89 seconds (1.668900 us/call) | |
| // | |
| // WaveletTree with MapperCont, wt_coder_binary, BSB_RRR | |
| // | |
| Encoded 605264456 symbols in 103738896 bytes -- 5.83 symbols per byte, 0.17 bytes per symbol | |
| Calculated 100000000 rank values in 235.18 seconds (2.351800 us/call) | |
| // | |
| // WaveletTree with MapperNone, wt_coder_binary, BSB_RRR | |
| // | |
| Encoded 605264456 symbols in 149084848 bytes -- 4.06 symbols per byte, 0.25 bytes per symbol | |
| Calculated 100000000 rank values in 425.69 seconds (4.256900 us/call) |
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