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r982: more accurate sum; output errors

This commit is contained in:
Heng Li 2020-04-14 16:18:53 -04:00
parent adde608a42
commit 29f67a1666
1 changed files with 5 additions and 3 deletions
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8
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.17-r981-dirty'; var paftools_version = '2.17-r982-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -941,13 +941,15 @@ function paf_asmgene(args)
} }
} }
for (var g in gene) { // count multi-copy genes for (var g in gene) { // count multi-copy genes
if (gene[g][0] == null || gene[g][0][0] == 1) continue; if (gene[g][0] == null || gene[g][0][0] <= 1) continue;
if (gene_nr[g] == null) continue; if (gene_nr[g] == null) continue;
if (auto_only && /^(chr)?[XY]$/.test(refpos[g][2])) continue; if (auto_only && /^(chr)?[XY]$/.test(refpos[g][2])) continue;
for (var i = 0; i < n_fn; ++i) { for (var i = 0; i < n_fn; ++i) {
if (gene[g][i] != null) rst[7][i] += gene[g][i][0];
if (gene[g][i] != null && gene[g][i][0] > 1) { if (gene[g][i] != null && gene[g][i][0] > 1) {
rst[6][i]++; rst[6][i]++;
rst[7][i] += gene[g][i][0]; } else if (print_err) {
print('d', header[i], gene[g][0][0], refpos[g].join("\t"));
} }
} }
} }