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more condition on length differences

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Heng Li
2024-11-17 19:45:46 -05:00
parent a10d4f4496
commit 618d33515e
1 changed files with 10 additions and 6 deletions
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misc/pafcluster.js
+10 -6
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@@ -84,7 +84,7 @@ function* k8_readline(fn) {
function merge_hits(b) { function merge_hits(b) {
if (b.length == 1) if (b.length == 1)
return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:b[0].min_cov, max_cov:b[0].max_cov, s1:b[0].s1, dv:b[0].dv }; return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:b[0].min_cov, max_cov:b[0].max_cov, cov1:b[0].cov1, cov2:b[0].cov2, s1:b[0].s1, dv:b[0].dv };
b.sort(function(x, y) { return x.st1 - y.st1 }); b.sort(function(x, y) { return x.st1 - y.st1 });
let f = [], bt = []; let f = [], bt = [];
for (let i = 0; i < b.length; ++i) for (let i = 0; i < b.length; ++i)
@@ -133,20 +133,22 @@ function merge_hits(b) {
const min_cov = cov1 < cov2? cov1 : cov2; const min_cov = cov1 < cov2? cov1 : cov2;
const max_cov = cov1 > cov2? cov1 : cov2; const max_cov = cov1 > cov2? cov1 : cov2;
//warn(d.length, b[0].name1, b[0].name2, min_cov, max_cov); //warn(d.length, b[0].name1, b[0].name2, min_cov, max_cov);
return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:min_cov, max_cov:max_cov, s1:max_f, dv:dv }; return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:min_cov, max_cov:max_cov, cov1:cov1, cov2:cov2, s1:max_f, dv:dv };
} }
function main(args) { function main(args) {
let opt = { min_cov:.8, max_dv:.015 }; let opt = { min_cov:.9, max_dv:.015, max_diff:20000 };
for (const o of getopt(args, "c:d:", [])) { for (const o of getopt(args, "c:d:e:", [])) {
if (o.opt == '-c') opt.min_cov = parseFloat(o.arg); if (o.opt == '-c') opt.min_cov = parseFloat(o.arg);
else if (o.opt == '-d') opt.max_dv = parseFloat(o.arg); else if (o.opt == '-d') opt.max_dv = parseFloat(o.arg);
else if (o.opt == '-e') opt.max_diff = parseFloat(o.arg);
} }
if (args.length == 0) { if (args.length == 0) {
print("Usage: pafcluster.js [options] <ava.paf>"); print("Usage: pafcluster.js [options] <ava.paf>");
print("Options:"); print("Options:");
print(` -c FLOAT min coverage [${opt.min_cov}]`); print(` -c FLOAT min coverage [${opt.min_cov}]`);
print(` -d FLOAT max divergence [${opt.max_dv}]`); print(` -d FLOAT max divergence [${opt.max_dv}]`);
print(` -e FLOAT max difference [${opt.max_diff}]`);
return; return;
} }
@@ -172,7 +174,7 @@ function main(args) {
const max_cov = cov1 > cov2? cov1 : cov2; const max_cov = cov1 > cov2? cov1 : cov2;
name2len[t[0]] = len1; name2len[t[0]] = len1;
name2len[t[5]] = len2; name2len[t[5]] = len2;
a.push({ name1:t[0], name2:t[5], len1:len1, len2:len2, min_cov:min_cov, max_cov:max_cov, s1:s1, dv:dv, st1:t[2], en1:t[3], st2:t[7], en2:t[8], blen:t[10] }); a.push({ name1:t[0], name2:t[5], len1:len1, len2:len2, min_cov:min_cov, max_cov:max_cov, s1:s1, dv:dv, cov1:cov1, cov2:cov2, st1:t[2], en1:t[3], st2:t[7], en2:t[8], blen:t[10] });
len[t[0]] = len1, len[t[5]] = len2; len[t[0]] = len1, len[t[5]] = len2;
} }
warn(`Read ${a.length} hits`); warn(`Read ${a.length} hits`);
@@ -206,7 +208,9 @@ function main(args) {
for (let i = 0; i < a.length; ++i) { for (let i = 0; i < a.length; ++i) {
if (a[i].name1 != max_name && a[i].name2 != max_name) if (a[i].name1 != max_name && a[i].name2 != max_name)
continue; continue;
if (a[i].min_cov >= opt.min_cov && a[i].dv <= opt.max_dv) const diff1 = a[i].len1 * (1.0 - a[i].cov1);
const diff2 = a[i].len2 * (1.0 - a[i].cov2);
if (a[i].min_cov >= opt.min_cov && a[i].dv <= opt.max_dv && diff1 <= opt.max_diff && diff2 <= opt.max_diff)
h[a[i].name1] = h[a[i].name2] = 1; h[a[i].name1] = h[a[i].name2] = 1;
} }
let n = 0; let n = 0;