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General doc improvements

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This commit is contained in:
Heng Li
2018-02-02 21:45:46 -05:00
parent 756379bf83
commit 3df5015668
2 changed files with 107 additions and 32 deletions
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misc/sim-eval.js
+10 -1
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@@ -46,7 +46,16 @@ while ((c = getopt(arguments, "Q:r:m:c")) != null) {
else if (c == 'c') cap_short_mapq = true;
}
var file = arguments.length == getopt.ind || arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
if (arguments.length == getopt.ind) {
warn("Usage: k8 sim-eval.js [options] <in.paf>|<in.sam>");
warn("Options:");
warn(" -r FLOAT mapping correct if overlap_length/union_length>FLOAT [" + ovlp_ratio + "]");
warn(" -Q INT print wrong mappings with mapQ>INT [don't print]");
warn(" -m INT 0: eval the longest aln only; 1: first aln only; 2: all primary aln [0]");
exit(1);
}
var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
var buf = new Bytes();
var tot = [], err = [];