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reduced the default -l and -b

This commit is contained in:
Heng Li 2021-07-19 17:25:11 -04:00
parent ead1cfbaca
commit c4fe52fb07
1 changed files with 5 additions and 5 deletions
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10
misc/mmphase.js
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@ -129,7 +129,7 @@ function find_het_sub(ev, a, opt)
last0_i = i; last0_i = i;
} else if (ev[i][2] == 1 && last0_i >= 0 && ev[i][0] < ev[last0_i][1]) { } else if (ev[i][2] == 1 && last0_i >= 0 && ev[i][0] < ev[last0_i][1]) {
if (ev[last0_i][1] - ev[last0_i][0] >= opt.min_mlen) { if (ev[last0_i][1] - ev[last0_i][0] >= opt.min_mlen) {
if (opt.dbg_ev) print(ev[last0_i].join("\t"), "|", ev[i].join("\t")); if (opt.dbg_ev) print("EV", ev[last0_i].join("\t"), "|", ev[i].join("\t"));
var e0 = ev[last0_i], hl = h[e0[3]]; var e0 = ev[last0_i], hl = h[e0[3]];
if (hl.length == 0 || hl[hl.length-1][0] != e0[0]) if (hl.length == 0 || hl[hl.length-1][0] != e0[0])
hl.push([e0[0], e0[1]]); hl.push([e0[0], e0[1]]);
@ -144,7 +144,7 @@ function find_het_sub(ev, a, opt)
sh += h[i][j][1] - h[i][j][0]; sh += h[i][j][1] - h[i][j][0];
for (var j = 0; j < d[i].length; ++j) for (var j = 0; j < d[i].length; ++j)
dh += d[i][j][1]; dh += d[i][j][1];
// // [start, end, index, #consistent, lenConsistent, #conflictive, lenConflictive, identity, mlen] // [start, end, index, #consistent, lenConsistent, #conflictive, lenConflictive, identity, mlen]
b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]]; b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]];
} }
return b; return b;
@ -184,7 +184,7 @@ function flt_utg_for_ec(b, opt)
} }
} }
function flt_utg_for_bin(b, opt) function flt_utg_for_bin(b, opt) // filter out alignments clearly on the wrong phase
{ {
var k = 0; var k = 0;
for (var i = 0; i < b.length; ++i) { for (var i = 0; i < b.length; ++i) {
@ -194,7 +194,7 @@ function flt_utg_for_bin(b, opt)
b.length = k; b.length = k;
} }
function ec_core(b, n_a, ev, buf, ecb) function ec_core(b, n_a, ev, buf, ecb) // error correction
{ {
var intv = []; var intv = [];
for (var i = 0; i < n_a; ++i) for (var i = 0; i < n_a; ++i)
@ -277,7 +277,7 @@ function process_paf(a, opt, fp_seq, buf, ecb)
function main(args) function main(args)
{ {
var c, opt = { min_rlen:20000, min_blen:10000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg_ev:false }; var c, opt = { min_rlen:5000, min_blen:5000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg_ev:false };
while ((c = getopt(args, "l:b:d:m:c:r:E")) != null) { while ((c = getopt(args, "l:b:d:m:c:r:E")) != null) {
if (c == 'l') opt.min_rlen = parseInt(getopt.arg); if (c == 'l') opt.min_rlen = parseInt(getopt.arg);
else if (c == 'b') opt.min_blen = parseInt(getopt.arg); else if (c == 'b') opt.min_blen = parseInt(getopt.arg);