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r1182: improved paftools.js compatibility

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Older k8/v8 can't use large memory. The previous change read large FASTA as
strings and might have problems. The new change tests k8 version.
This commit is contained in:
Heng Li
2023-10-30 16:37:29 -04:00
parent ab717023b6
commit bc588c0eeb
1 changed files with 48 additions and 23 deletions
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71
misc/paftools.js
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.26-r1175';
var paftools_version = '2.26-r1182-dirty';
/*****************************
***** Library functions *****
@@ -133,26 +133,50 @@ Interval.find_ovlp = function(a, st, en)
function fasta_read(fn)
{
var h = {}, gt = '>'.charCodeAt(0);
var h = {}, seqlen = [];
var buf = new Bytes();
var file = fn == '-'? new File() : new File(fn);
var buf = new Bytes(), seq = null, name = null, seqlen = [];
while (file.readline(buf) >= 0) {
if (buf[0] == gt) {
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq;
name = seq = null;
}
var m, line = buf.toString();
if ((m = /^>(\S+)/.exec(line)) != null) {
name = m[1];
seq = new Bytes();
}
} else seq.set(buf);
}
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq;
if (typeof k8_version == "undefined") { // for k8-0.x
var seq = null, name = null, gt = '>'.charCodeAt(0);
while (file.readline(buf) >= 0) {
if (buf[0] == gt) {
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq;
name = seq = null;
}
var m, line = buf.toString();
if ((m = /^>(\S+)/.exec(line)) != null) {
name = m[1];
seq = new Bytes();
}
} else seq.set(buf);
}
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq;
}
} else { // for k8-1.x
var seq = null, name = null;
while (file.readline(buf) >= 0) {
var line = buf.toString();
if (line[0] == ">") {
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq.toString();
name = seq = null;
}
var m;
if ((m = /^>(\S+)/.exec(line)) != null) {
name = m[1];
seq = new Bytes();
}
} else seq.set(line);
}
if (seq != null && name != null) {
seqlen.push([name, seq.length]);
h[name] = seq.toString();
}
}
buf.destroy();
file.close();
@@ -161,8 +185,9 @@ function fasta_read(fn)
function fasta_free(fa)
{
for (var name in fa)
fa[name].destroy();
if (typeof k8_version == "undefined")
for (var name in fa)
fa[name].destroy();
}
Bytes.prototype.reverse = function()
@@ -379,7 +404,7 @@ function paf_call(args)
} else if (o[1] > 0) { // shouldn't happen in theory
if (fa[o[0]] == null) throw Error('sequence "' + o[0] + '" is absent from the reference FASTA');
if (o[1] >= fa[o[0]].length) throw Error('position ' + o[1] + ' exceeds the length of sequence "' + o[0] + '"');
var ref = String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase();
var ref = typeof k8_version == "undefined"? String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase() : fa[o[0]][o[1]-1].toUpperCase();
if (o[5] == '-') // insertion
v = [o[0], o[1], '.', ref, ref + o[6].toUpperCase()];
else // deletion