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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/gff2bed.js
Regular → Executable
+3 -1
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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')
@@ -99,7 +101,7 @@ function print_bed12(exons, cds_st, cds_en, is_short)
var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name) "([^"]+)";/g;
var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g;
var buf = new Bytes();
var file = new File(arguments[getopt.ind]);
var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
while (file.readline(buf) >= 0) {