-x sr is silently identical to -x adap - #63
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MB_F_ADAP was set unconditionally, overriding the conditional added in r234. Also drop two statements made dead by the reset in mb_opt_preset().
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-x srgives identical output to-x adap.mb_opt_presetsetsMB_F_ADAPunconditionally two lines below the gated set that r234 added when it separated the two presets, so both end up at flag0x4048andsris unreachable. The man page hasadapas-xsr --adap=yes, which is not currently true.Deleting the stray line restores
sr. Two no-ops go with it:mb_opt_presetresetsopton entry, so themb_opt_resetinmb_opt_initand the~MB_F_PEin thelrbranch do nothing. Drop those two if you prefer the one-line fix.On 1M HG002 WGS pairs,
-x adapis byte-identical to before;-x srmoves 0.11% of pairs, 69% of them at MAPQ <= 1.If you meant the two presets to stay identical, the gated line should go instead and the man page needs correcting.