fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-05 01:08:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

reverted to the previous paftools.js

Browse Source
This commit is contained in:
Heng Li
2023-10-30 16:24:18 -04:00
parent 9506e7ac3f
commit ab717023b6
1 changed files with 15 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files
misc/paftools.js
+15 -11
View File
@@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.26-r1180-dirty'; var paftools_version = '2.26-r1175';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@@ -133,35 +133,38 @@ Interval.find_ovlp = function(a, st, en)
function fasta_read(fn) function fasta_read(fn)
{ {
var h = {}; var h = {}, gt = '>'.charCodeAt(0);
var file = fn == '-'? new File() : new File(fn); var file = fn == '-'? new File() : new File(fn);
var buf = new Bytes(), seq = null, name = null, seqlen = []; var buf = new Bytes(), seq = null, name = null, seqlen = [];
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var line = buf.toString(); if (buf[0] == gt) {
if (line[0] == '>') {
if (seq != null && name != null) { if (seq != null && name != null) {
seqlen.push([name, seq.length]); seqlen.push([name, seq.length]);
h[name] = seq.toString(); h[name] = seq;
seq.destroy();
name = seq = null; name = seq = null;
} }
var m; var m, line = buf.toString();
if ((m = /^>(\S+)/.exec(line)) != null) { if ((m = /^>(\S+)/.exec(line)) != null) {
name = m[1]; name = m[1];
seq = new Bytes(); seq = new Bytes();
} }
} else seq.set(line); } else seq.set(buf);
} }
if (seq != null && name != null) { if (seq != null && name != null) {
seqlen.push([name, seq.length]); seqlen.push([name, seq.length]);
h[name] = seq.toString(); h[name] = seq;
seq.destroy();
} }
buf.destroy(); buf.destroy();
file.close(); file.close();
return [h, seqlen]; return [h, seqlen];
} }
function fasta_free(fa)
{
for (var name in fa)
fa[name].destroy();
}
Bytes.prototype.reverse = function() Bytes.prototype.reverse = function()
{ {
for (var i = 0; i < this.length>>1; ++i) { for (var i = 0; i < this.length>>1; ++i) {
@@ -376,7 +379,7 @@ function paf_call(args)
} else if (o[1] > 0) { // shouldn't happen in theory } 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 (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] + '"'); if (o[1] >= fa[o[0]].length) throw Error('position ' + o[1] + ' exceeds the length of sequence "' + o[0] + '"');
var ref = fa[o[0]][o[1]-1].toUpperCase(); var ref = String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase();
if (o[5] == '-') // insertion if (o[5] == '-') // insertion
v = [o[0], o[1], '.', ref, ref + o[6].toUpperCase()]; v = [o[0], o[1], '.', ref, ref + o[6].toUpperCase()];
else // deletion else // deletion
@@ -557,6 +560,7 @@ function paf_call(args)
buf.destroy(); buf.destroy();
file.close(); file.close();
if (fa != null) fasta_free(fa);
} }
function paf_asmstat(args) function paf_asmstat(args)