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support both SAM and PAF as input

This commit is contained in:
Heng Li 2017-12-02 21:57:19 -05:00
parent e575f884e1
commit 76206f574f
1 changed files with 41 additions and 39 deletions
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80
misc/splice2bed.js
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@ -43,16 +43,15 @@ function print_lines(a, fmt) {
if (fmt == "bed") {
var n_pri = 0;
for (var i = 0; i < a.length; ++i)
if (a[i][9] == 0) ++n_pri;
if (a[i][8] == 0) ++n_pri;
if (n_pri > 1) {
for (var i = 0; i < a.length; ++i)
if (a[i][9] == 0) a[i][9] = 1;
if (a[i][8] == 0) a[i][8] = 1;
} else if (n_pri == 0) {
warn("Warning: " + a[0][0] + " doesn't have a primary alignment");
warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
}
for (var i = 0; i < a.length; ++i) {
a[i][9] = colors[a[i][9]];
a[i].shift();
a[i][8] = colors[a[i][8]];
print(a[i].join("\t"));
}
}
@ -61,23 +60,15 @@ function print_lines(a, fmt) {
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;
var c, fmt = "bed";
while ((c = getopt(args, "f:")) != null) {
if (c == 'f') fmt = getopt.arg;
}
if (getopt.ind == args.length && !hdr_only) {
warn("Usage: k8 splice2bed.js [options] <in.paf>");
if (getopt.ind == args.length) {
warn("Usage: k8 splice2bed.js <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 = [];
@ -85,12 +76,12 @@ function main(args) {
var line = buf.toString();
if (line.charAt(0) == '@') continue; // skip SAM header lines
var t = line.split("\t");
var is_pri = false, cigar = null, a1;
if (a.length && a[0][3] != t[0]) {
print_lines(a, fmt);
a = [];
}
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);
@ -98,24 +89,35 @@ function main(args) {
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(",")+","]);
a1 = [t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4]];
} else if (t.length >= 10) {
var flag = parseInt(t[1]);
if ((flag&4) || a[2] == '*') continue;
cigar = t[5];
is_pri = (flag&0x100)? false : true;
a1 = [t[2], parseInt(t[3])-1, null, t[0], 1000, (flag&16)? '-' : '+'];
} else {
throw Error("unrecognized input format");
}
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);
// write the BED12 line
if (a1[2] == null) a1[2] = a1[1] + x;
a1.push(a1[1], a1[2]); // thick start/end is the same as start/end
a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
a.push(a1);
}
print_lines(a, fmt);
buf.destroy();