pslReps in.psl out.psl out.psr
This tool is part of UCSC Genome Browser's utilities.
where in.psl is an alignment file generated by psLayout and
sorted by pslSort, out.psl is the best alignment output
and out.psr contains repeat info
-nohead don't add PSL header
-ignoreSize Will not weigh in favor of larger alignments so much
-noIntrons Will not penalize for not having introns when calculating
-singleHit Takes single best hit, not splitting into parts
-minCover=0.N minimum coverage to output. Default is 0.
-ignoreNs Ignore 'N's when calculating minCover.
-minAli=0.N minimum alignment ratio
default is 0.93
-nearTop=0.N how much can deviate from top and be taken
default is 0.01
-minNearTopSize=N Minimum size of alignment that is near top
for alignment to be kept. Default 30.
-coverQSizes=file Tab-separate file with effective query sizes.
When used with -minCover, this allows polyAs
to be excluded from the coverage calculation
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