mcshane / capmq Goto Github PK
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License: Other
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-C option accepts negative values but represents them as unsigned
The range of values provided for capQ are not checked and can result in setting MAPQ to zero:
$ ./capmq -C -256 test1.sam
@HD VN:1.4
@PG ID:capmq PN:capmq VN:0.3-2-g1be2b12-dirty CL:./capmq -C -256 test1.sam DS:cap map quality values
@SQ SN:alpha LN:100
@RG ID:a LB:1 SM:s1
@RG ID:b LB:1 SM:s1
r1 99 alpha 1 0 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:a NM:i:0 om:i:45
r1 147 alpha 66 0 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:a NM:i:0 om:i:46
r1 99 alpha 1 0 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:b NM:i:0 om:i:47
r1 147 alpha 66 0 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:b NM:i:0 om:i:48
r1 99 alpha 1 0 35M = 66 100 TGTCATAGTAATCCGGTTGGGAGTCCGAGGTGGGG * RG:Z:b NM:i:0 om:i:4
r1 147 alpha 66 0 35M = 1 -100 AGAACTTTGCAGCCATATCTCCAAGACATGTATCC * RG:Z:b NM:i:0 om:i:4
capmq with -f and -m raises existing mapping qualities
when capmq is run with -f and -m min options, it raises the mapping quality of existing low mapping quality reads to min. this is probably not the desired behaviour.
verbose not implemented
the usage lists a -v for verbose output, but it doesn't work:
$ capmq -v
Unknown option: 'v'
...
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