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r1189: fixed an out-of-memory issue

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Resolves #1166
This commit is contained in:
Heng Li
2024-03-11 10:14:20 -04:00
parent 940388f8e4
commit 0efc886012
1 changed files with 5 additions and 4 deletions
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misc/paftools.js
+5 -4
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.26-r1182-dirty'; var paftools_version = '2.26-r1189-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@@ -163,7 +163,7 @@ function fasta_read(fn)
if (line[0] == ">") { 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] = new Uint8Array(seq.buffer);
name = seq = null; name = seq = null;
} }
var m; var m;
@@ -175,7 +175,7 @@ function fasta_read(fn)
} }
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] = new Uint8Array(seq.buffer);
} }
} }
buf.destroy(); buf.destroy();
@@ -188,6 +188,7 @@ function fasta_free(fa)
if (typeof k8_version == "undefined") if (typeof k8_version == "undefined")
for (var name in fa) for (var name in fa)
fa[name].destroy(); fa[name].destroy();
// FIXME: for k8-1.0, sequences are not freed. This is ok for now but not general.
} }
Bytes.prototype.reverse = function() Bytes.prototype.reverse = function()
@@ -404,7 +405,7 @@ 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 = typeof k8_version == "undefined"? String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase() : 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