zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

convert spliced PAF to BED

This commit is contained in:
Heng Li 2017-12-02 21:23:41 -05:00
parent 571161d5a2
commit e575f884e1
1 changed files with 125 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

125
misc/splice2bed.js 100644
View File

@ -0,0 +1,125 @@
var getopt = function(args, ostr) {
var oli; // option letter list index
if (typeof(getopt.place) == 'undefined')
getopt.ind = 0, getopt.arg = null, getopt.place = -1;
if (getopt.place == -1) { // update scanning pointer
if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
getopt.place = -1;
return null;
}
if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
++getopt.ind;
getopt.place = -1;
return null;
}
}
var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
if (optopt == '-') return null; // if the user didn't specify '-' as an option, assume it means null.
if (getopt.place < 0) ++getopt.ind;
return '?';
}
if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
getopt.arg = null;
if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
} else { // need an argument
if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
getopt.arg = args[getopt.ind].substr(getopt.place);
else if (args.length <= ++getopt.ind) { // no arg
getopt.place = -1;
if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
return '?';
} else getopt.arg = args[getopt.ind]; // white space
getopt.place = -1;
++getopt.ind;
}
return optopt;
}
var colors = ["0,128,255", "255,0,0", "0,192,0"];
function print_lines(a, fmt) {
if (a.length == 0) return;
if (fmt == "bed") {
var n_pri = 0;
for (var i = 0; i < a.length; ++i)
if (a[i][9] == 0) ++n_pri;
if (n_pri > 1) {
for (var i = 0; i < a.length; ++i)
if (a[i][9] == 0) a[i][9] = 1;
} else if (n_pri == 0) {
warn("Warning: " + a[0][0] + " doesn't have a primary alignment");
}
for (var i = 0; i < a.length; ++i) {
a[i][9] = colors[a[i][9]];
a[i].shift();
print(a[i].join("\t"));
}
}
a.length = 0;
}
function main(args) {
var re = /(\d+)([MIDNSH])/g;
var c, fmt = "bed", with_hdr = false, hdr_only = false, name = 'splice2bed', pos = null;
while ((c = getopt(args, "Hhn:p:")) != null) {
if (c == 'h') with_hdr = true;
else if (c == 'p') pos = getopt.arg;
else if (c == 'H') with_hdr = hdr_only = true;
else if (c == 'n') name = getopt.arg;
}
if (getopt.ind == args.length && !hdr_only) {
warn("Usage: k8 splice2bed.js [options] <in.paf>");
exit(1);
}
if (with_hdr) {
if (pos != null)
print('browser position ' + pos);
print('track name=' + name + ' useScore=1 visibility=2 itemRgb="On"');
}
if (hdr_only) return;
var file = new File(args[getopt.ind]);
var buf = new Bytes();
var a = [];
while (file.readline(buf) >= 0) {
var line = buf.toString();
if (line.charAt(0) == '@') continue; // skip SAM header lines
var t = line.split("\t");
if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) {
if (a.length && a[0][0] != t[0]) {
print_lines(a, fmt);
a = [];
}
var is_pri = false, cigar = null;
for (var i = 12; i < t.length; ++i) {
if (t[i].substr(0, 5) == 'cg:Z:') {
cigar = t[i].substr(5);
} else if (t[i].substr(0, 5) == 's2:i:') {
is_pri = true;
}
}
if (cigar == null) throw Error("missing CIGAR");
var m, x0 = 0, x = 0, bs = [], bl = [];
while ((m = re.exec(cigar)) != null) {
if (m[2] == 'M' || m[2] == 'D') {
x += parseInt(m[1]);
} else if (m[2] == 'N') {
bs.push(x0);
bl.push(x - x0);
x += parseInt(m[1]);
x0 = x;
}
}
bs.push(x0);
bl.push(x - x0);
a.push([t[0], t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4], t[7], t[8], is_pri? 0:2, bs.length, bl.join(",")+",", bs.join(",")+","]);
} else {
throw Error("unrecognized input format");
}
}
print_lines(a, fmt);
buf.destroy();
file.close();
}
main(arguments);