Open brian-odonovan opened 7 months ago
I am looking at some very strange alignments and the only explanation I can come up with is that the -np flag isnt working appropriately:
I have the argstring as follows: -k 10 ---ignore-quals --mp 1,1 --sp 1,1 --np 1 --score-min L,0,-0.25
-k 10 ---ignore-quals --mp 1,1 --sp 1,1 --np 1 --score-min L,0,-0.25
How are the XM and NM tags reported at 105 (should count at mismatches with a penalty -1) but the alignment score is still -33 ??
SL-NVT:HG5GGDRX3230926:HG5GGDRX3:1:2103:25328:27007 0 CP118289.1 2188408 60 128M22S * 0 0 CCCCCCCCCCCCCCCCCCCCCCCATTTTCAAGCAGAAGACGGCATACGAGATGTCGCATCGTGACTGGAGTTCAACGTGTGCTCTTCCGATCTCTCCAAAACACTTCCATTCCGTGTAAATCAGATCTATAGTGTTGGTTATGATTTCGG FFFFFFFFFFFFFFFFF::,,,,,,FFF:FFFFF:FFFFFFFFFFFFF,FFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-43 ZS:i:-94 XN:i:0 XM:i:105 XO:i:0 XG:i:0 NM:i:105 MD:Z:23C0C0C0C0C0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0 YT:Z:UU NH:i:1
I personally looked at the alignment for some and they are reported like this:
I am looking at some very strange alignments and the only explanation I can come up with is that the -np flag isnt working appropriately:
I have the argstring as follows:
-k 10 ---ignore-quals --mp 1,1 --sp 1,1 --np 1 --score-min L,0,-0.25How are the XM and NM tags reported at 105 (should count at mismatches with a penalty -1) but the alignment score is still -33 ??
SL-NVT:HG5GGDRX3230926:HG5GGDRX3:1:2103:25328:27007 0 CP118289.1 2188408 60 128M22S * 0 0 CCCCCCCCCCCCCCCCCCCCCCCATTTTCAAGCAGAAGACGGCATACGAGATGTCGCATCGTGACTGGAGTTCAACGTGTGCTCTTCCGATCTCTCCAAAACACTTCCATTCCGTGTAAATCAGATCTATAGTGTTGGTTATGATTTCGG FFFFFFFFFFFFFFFFF::,,,,,,FFF:FFFFF:FFFFFFFFFFFFF,FFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-43 ZS:i:-94 XN:i:0 XM:i:105 XO:i:0 XG:i:0 NM:i:105 MD:Z:23C0C0C0C0C0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0N0 YT:Z:UU NH:i:1I personally looked at the alignment for some and they are reported like this: