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r895: option in asmgene to count autosomal only

This commit is contained in:
Heng Li 2018-12-14 10:36:47 -05:00
parent ea2b1c5b2a
commit 5b2fdfff9c
1 changed files with 6 additions and 3 deletions
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9
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.14-r893-dirty'; var paftools_version = '2.14-r895-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -801,11 +801,12 @@ function paf_asmstat(args)
function paf_asmgene(args) function paf_asmgene(args)
{ {
var c, opt = { min_cov:0.99, min_iden:0.99 }, print_err = false; var c, opt = { min_cov:0.99, min_iden:0.99 }, print_err = false, auto_only = false;
while ((c = getopt(args, "i:c:e")) != null) while ((c = getopt(args, "i:c:ea")) != null)
if (c == 'i') opt.min_iden = parseFloat(getopt.arg); if (c == 'i') opt.min_iden = parseFloat(getopt.arg);
else if (c == 'c') opt.min_cov = parseFloat(getopt.arg); else if (c == 'c') opt.min_cov = parseFloat(getopt.arg);
else if (c == 'e') print_err = true; else if (c == 'e') print_err = true;
else if (c == 'a') auto_only = true;
var n_fn = args.length - getopt.ind; var n_fn = args.length - getopt.ind;
if (n_fn < 2) { if (n_fn < 2) {
@ -813,6 +814,7 @@ function paf_asmgene(args)
print("Options:"); print("Options:");
print(" -i FLOAT min identity [" + opt.min_iden + "]"); print(" -i FLOAT min identity [" + opt.min_iden + "]");
print(" -c FLOAT min coverage [" + opt.min_cov + "]"); print(" -c FLOAT min coverage [" + opt.min_cov + "]");
print(" -a only evaluate genes mapped to the autosomes");
print(" -e print fragmented/missing genes"); print(" -e print fragmented/missing genes");
exit(1); exit(1);
} }
@ -895,6 +897,7 @@ function paf_asmgene(args)
for (var g in gene) { for (var g in gene) {
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;
for (var i = 0; i < n_fn; ++i) { for (var i = 0; i < n_fn; ++i) {
if (gene[g][i] == null) { if (gene[g][i] == null) {
rst[4][i]++; rst[4][i]++;