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r1191: fixed wrong reverse() and revcomp()

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due to k8 incompatibility. Resolves #1161
This commit is contained in:
Heng Li
2024-03-11 22:09:01 -04:00
parent fcd4df2a73
commit ba60aac6f6
1 changed files with 31 additions and 11 deletions
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misc/paftools.js
+31 -11
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.26-r1189-dirty'; var paftools_version = '2.26-r1191-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@@ -193,10 +193,19 @@ function fasta_free(fa)
Bytes.prototype.reverse = function() Bytes.prototype.reverse = function()
{ {
for (var i = 0; i < this.length>>1; ++i) { if (typeof k8_version === "undefined") { // k8-0.x
var tmp = this[i]; for (var i = 0; i < this.length>>1; ++i) {
this[i] = this[this.length - i - 1]; var tmp = this[i];
this[this.length - i - 1] = tmp; this[i] = this[this.length - i - 1];
this[this.length - i - 1] = tmp;
}
} else { // k8-1.x
var buf = new Uint8Array(this.buffer);
for (var i = 0; i < buf.length>>1; ++i) {
var tmp = buf[i];
buf[i] = buf[buf.length - i - 1];
buf[buf.length - i - 1] = tmp;
}
} }
} }
@@ -211,13 +220,24 @@ Bytes.prototype.revcomp = function()
for (var i = 0; i < s1.length; ++i) for (var i = 0; i < s1.length; ++i)
Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i); Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
} }
for (var i = 0; i < this.length>>1; ++i) { if (typeof k8_version === "undefined") { // k8-0.x
var tmp = this[this.length - i - 1]; for (var i = 0; i < this.length>>1; ++i) {
this[this.length - i - 1] = Bytes.rctab[this[i]]; var tmp = this[this.length - i - 1];
this[i] = Bytes.rctab[tmp]; this[this.length - i - 1] = Bytes.rctab[this[i]];
this[i] = Bytes.rctab[tmp];
}
if (this.length&1)
this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
} else { // k8-1.x
var buf = new Uint8Array(this.buffer);
for (var i = 0; i < buf.length>>1; ++i) {
var tmp = buf[buf.length - i - 1];
buf[buf.length - i - 1] = Bytes.rctab[buf[i]];
buf[i] = Bytes.rctab[tmp];
}
if (buf.length&1)
buf[buf.length>>1] = Bytes.rctab[buf[buf.length>>1]];
} }
if (this.length&1)
this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
} }
/******************** /********************