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paftools-r713: fixed bug for cov1 regions

This commit is contained in:
Heng Li 2018-02-16 12:20:46 -05:00
parent 54a42aafe5
commit e1f18690f6
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
// Version: r702 var paftools_version = 'r713';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -362,6 +362,7 @@ function paf_call(args)
for (var i = 6; i <= 11; ++i) for (var i = 6; i <= 11; ++i)
t[i] = parseInt(t[i]); t[i] = parseInt(t[i]);
if (t[10] < min_cov_len || t[11] < min_mapq) continue; if (t[10] < min_cov_len || t[11] < min_mapq) continue;
print(t[0], t[7], t[8], c1_start, c1_end);
for (var i = 1; i <= 3; ++i) for (var i = 1; i <= 3; ++i)
t[i] = parseInt(t[i]); t[i] = parseInt(t[i]);
var ctg = t[5], x = t[7], end = t[8]; var ctg = t[5], x = t[7], end = t[8];
@ -381,13 +382,13 @@ function paf_call(args)
} }
c1_start = c1_end, c1_end = end; c1_start = c1_end, c1_end = end;
c1_counted = (t[10] >= min_var_len); c1_counted = (t[10] >= min_var_len);
} else { // contained } else if (end > c1_start) { // contained
if (c1_counted && x > c1_start) { if (c1_counted && x > c1_start) {
c1_len += x - c1_start; c1_len += x - c1_start;
print('R', c1_ctg, c1_start, x); print('R', c1_ctg, c1_start, x);
} }
c1_start = end; c1_start = end;
} } // else, the alignment precedes the cov1 region; do nothing
// output variants ahead of this alignment // output variants ahead of this alignment
while (out.length) { while (out.length) {
if (out[0][0] != ctg || out[0][2] <= x) { if (out[0][0] != ctg || out[0][2] <= x) {
@ -1837,6 +1838,7 @@ function main(args)
print(" liftover simplistic liftOver"); print(" liftover simplistic liftOver");
print(" call call variants from asm-to-ref alignment with the cs tag"); print(" call call variants from asm-to-ref alignment with the cs tag");
print(" bedcov compute the number of bases covered"); print(" bedcov compute the number of bases covered");
print(" version print paftools.js version");
print(""); print("");
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ"); print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
print(" mason2fq convert mason2-simulated SAM to FASTQ"); print(" mason2fq convert mason2-simulated SAM to FASTQ");
@ -1861,6 +1863,7 @@ function main(args)
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args); else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
else if (cmd == 'junceval') paf_junceval(args); else if (cmd == 'junceval') paf_junceval(args);
else if (cmd == 'ov-eval') paf_ov_eval(args); else if (cmd == 'ov-eval') paf_ov_eval(args);
else if (cmd == 'version') print(paftools_version);
else throw Error("unrecognized command: " + cmd); else throw Error("unrecognized command: " + cmd);
} }