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allow to convert read names 

ONT read names are just too long and too hard to compress
This commit is contained in:
Heng Li 2018-01-05 22:05:15 -05:00
parent a465a920ec
commit e9607fcd9b
1 changed files with 19 additions and 2 deletions
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21
misc/splice2bed.js
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@ -60,15 +60,29 @@ function print_lines(a, fmt) {
function main(args) { function main(args) {
var re = /(\d+)([MIDNSH])/g; var re = /(\d+)([MIDNSH])/g;
var c, fmt = "bed"; var c, fmt = "bed", fn_name_conv = null;
while ((c = getopt(args, "f:")) != null) { while ((c = getopt(args, "f:n:")) != null) {
if (c == 'f') fmt = getopt.arg; if (c == 'f') fmt = getopt.arg;
else if (c == 'n') fn_name_conv = getopt.arg;
} }
if (getopt.ind == args.length) { if (getopt.ind == args.length) {
warn("Usage: k8 splice2bed.js <in.paf>"); warn("Usage: k8 splice2bed.js <in.paf>");
exit(1); exit(1);
} }
var conv = null;
if (fn_name_conv != null) {
conv = new Map();
var file = new File(fn_name_conv);
var buf = new Bytes();
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
conv.put(t[0], t[1]);
}
buf.destroy();
file.close();
}
var file = new File(args[getopt.ind]); var file = new File(args[getopt.ind]);
var buf = new Bytes(); var buf = new Bytes();
var a = []; var a = [];
@ -77,6 +91,8 @@ function main(args) {
if (line.charAt(0) == '@') continue; // skip SAM header lines if (line.charAt(0) == '@') continue; // skip SAM header lines
var t = line.split("\t"); var t = line.split("\t");
var is_pri = false, cigar = null, a1; var is_pri = false, cigar = null, a1;
var qname = conv != null? conv.get(t[0]) : null;
if (qname != null) t[0] = qname;
if (a.length && a[0][3] != t[0]) { if (a.length && a[0][3] != t[0]) {
print_lines(a, fmt); print_lines(a, fmt);
a = []; a = [];
@ -122,6 +138,7 @@ function main(args) {
print_lines(a, fmt); print_lines(a, fmt);
buf.destroy(); buf.destroy();
file.close(); file.close();
if (conv != null) conv.destroy();
} }
main(arguments); main(arguments);