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Release minimap2-2.23 (r1111)

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This commit is contained in:
Heng Li
2021-11-18 17:11:48 -05:00
parent ac334639ce
commit d0cff3eb36
8 changed files with 54 additions and 13 deletions
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misc/paftools.js
+27 -4
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.22-r1101';
var paftools_version = '2.23-r1111';
/*****************************
***** Library functions *****
@@ -1532,12 +1532,13 @@ function paf_view(args)
function paf_gff2bed(args)
{
var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false;
while ((c = getopt(args, "u:sgj")) != null) {
var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false, output_gene = false;
while ((c = getopt(args, "u:sgjG")) != null) {
if (c == 'u') fn_ucsc_fai = getopt.arg;
else if (c == 's') is_short = true;
else if (c == 'g') keep_gff = true;
else if (c == 'j') print_junc = true;
else if (c == 'G') output_gene = true;
}
if (getopt.ind == args.length) {
@@ -1605,8 +1606,10 @@ function paf_gff2bed(args)
print(a[0][0], st, en, name, 1000, a[0][3], cds_st, cds_en, color, a.length, sizes.join(",") + ",", starts.join(",") + ",");
}
var re_gtf = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name) "([^"]+)";/g;
var re_gtf = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name) "([^"]+)";/g;
var re_gff3 = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name)=([^;]+)/g;
var re_gtf_gene = /\b(gene_id|gene_type|gene_name) "([^;]+)";/g;
var re_gff3_gene = /\b(gene_id|gene_type|source_gene|gene_biotype|gene_name)=([^;]+);/g;
var buf = new Bytes();
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
@@ -1620,6 +1623,26 @@ function paf_gff2bed(args)
continue;
}
if (t[0].charAt(0) == '#') continue;
if (output_gene) {
var id = null, src = null, biotype = null, type = "", name = "N/A";
if (t[2] != "gene") continue;
while ((m = re_gtf_gene.exec(t[8])) != null) {
if (m[1] == "gene_id") id = m[2];
else if (m[1] == "gene_type") type = m[2];
else if (m[1] == "gene_name") name = m[2];
}
while ((m = re_gff3_gene.exec(t[8])) != null) {
if (m[1] == "gene_id") id = m[2];
else if (m[1] == "source_gene") src = m[2];
else if (m[1] == "gene_type") type = m[2];
else if (m[1] == "gene_biotype") biotype = m[2];
else if (m[1] == "gene_name") name = m[2];
}
if (src != null) id = src;
if (type == "" && biotype != null) type = biotype;
print(t[0], parseInt(t[3]) - 1, t[4], [id, type, name].join("|"), 1000, t[6]);
continue;
}
if (t[2] != "CDS" && t[2] != "exon") continue;
t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]);