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some compare result of minimap2 '-x sr' mode of v2.18 and v2.20 #776
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Thanks. On my dataset, I didn't see this. v2.20 is slightly more accurate on the contrary. Perhaps a difference between datasets. Either way, you may try to add |
in this dataset, '-xsr -e0' help the a) performance, but few changes in the b) mapping result. v2.20 with -xsr -e0 There is no '-e0' option in minimap2 v2.18, so no test result of v2.18 with -e0 option. |
Could you check the github HEAD to see if this is fixed on your data? Thanks. |
PS: if it is ok on your data, I will release v2.21 for this bug fix. |
Very good result with this fix. minimap2 2.20 r1069 without -e0 minimap2 2.20 r1069 with -e0 By the way, in the coming 2.21 release, please change the man file too? Best regards |
Thanks, @jmarshall. I will wait. I need to run some large-scale tests anyway before each release. It will take some time. |
for PE short reads. An interesting omission. Resolves lh3#776
some compare result of minimap2 '-x sr' mode of v2.18 and v2.20
genome: GRCh38.p13
data: Illumina PE150
a) performance: big change in runtime.
v2.18
real 213.72(3:33.72), user 12295.66, sys 169.28
v2.20
real 323.90(5:23.90), user 17924.58, sys 225.08
but memory usage is almost same.
b) mapping result: big change in 'properly paired %' and 'singletons %'
v2.18
mapped % 97.16%
mapq>=1 % 92.69%
properly paired % 95.98%
singletons % 0.30%
v2.20
mapped % 96.34%
mapq>=1 % 92.01%
properly paired % 92.63%
singletons % 1.07%
c) misc
in man file, '-r50' is in '-x sr' mode,
but '-r100' is in source(mo->bw = mo->bw_long = 100;).
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