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r213: renamed trio binning output files

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Heng Li
2020-04-09 20:40:01 -04:00
parent c3f032da37
commit 7a35bd7fcc
5 changed files with 97 additions and 90 deletions
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CommandLines.cpp
+5 -5
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@@ -50,8 +50,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " Trio-partition:\n");
fprintf(stderr, " -P FILE paternal trio index generated by \"yak count\" []\n");
fprintf(stderr, " -M FILE maternal trio index generated by \"yak count\" []\n");
fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n");
fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\n");
fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
@@ -313,7 +313,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:", long_options)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -339,8 +339,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'b') asm_opt->required_read_name = opt.arg;
else if (c == 'c') asm_opt->min_cnt = atoi(opt.arg);
else if (c == 'd') asm_opt->mid_cnt = atoi(opt.arg);
else if (c == 'P') asm_opt->pat_index = opt.arg;
else if (c == 'M') asm_opt->mat_index = opt.arg;
else if (c == '1' || c == 'P') asm_opt->pat_index = opt.arg; // -P/-M reserved for backward compatibility
else if (c == '2' || c == 'M') asm_opt->mat_index = opt.arg;
else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);