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Documented some k8 scripts; more coming

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This commit is contained in:
Heng Li
2018-02-02 13:57:08 -05:00
parent 35d3e064bf
commit ddc31f57ba
8 changed files with 77 additions and 24 deletions
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misc/splice2bed.js
Regular → Executable
+4 -2
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@@ -1,3 +1,5 @@
#!/usr/bin/env k8
var getopt = function(args, ostr) {
var oli; // option letter list index
if (typeof(getopt.place) == 'undefined')
@@ -66,7 +68,7 @@ function main(args) {
else if (c == 'n') fn_name_conv = getopt.arg;
}
if (getopt.ind == args.length) {
warn("Usage: k8 splice2bed.js <in.paf>");
warn("Usage: k8 splice2bed.js <in.paf>|<in.sam>");
exit(1);
}
@@ -83,7 +85,7 @@ function main(args) {
file.close();
}
var file = new File(args[getopt.ind]);
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
var buf = new Bytes();
var a = [];
while (file.readline(buf) >= 0) {