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s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
https://s4hts.github.io/HTStream/
Apache License 2.0
49 stars 9 forks source link

threaded overlapper #226

Closed joe-angell closed 4 years ago

joe-angell commented 4 years ago

refs #204

Tested on a 800k dataset, got the same result as master.

time ./hts_Overlapper/hts_Overlapper -1 ../data/lin2_R1.fastq.gz -2 ../data/lin2_R2.fastq.gz -p 4 > /dev/null
./hts_Overlapper/hts_Overlapper -1 ../data/lin2_R1.fastq.gz -2  -p 4 >   67.22s user 5.73s system 529% cpu 13.780 total
 vs master:
time ./hts_Overlapper/hts_Overlapper -1 ../data/lin2_R1.fastq.gz -2 ../data/lin2_R2.fastq.gz > /dev/null     
./hts_Overlapper/hts_Overlapper -1 ../data/lin2_R1.fastq.gz -2  > /dev/null  42.98s user 1.17s system 99% cpu 44.386 total