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require >=2 copies for regular tandem repeats
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Yan Gao
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Nov 17, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -55,6 +55,8 @@ data/* | |
| .tags | ||
| tags | ||
| cscope.* | ||
| .vscode | ||
| src/.tags | ||
| src/tags | ||
| src/cscope* | ||
| src/.vscode | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -10,7 +10,7 @@ | |
| #include "kseq.h" | ||
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| const char PROG[20] = "TideHunter"; | ||
| const char VERSION[20] = "1.5.4"; | ||
| const char VERSION[20] = "1.5.5"; | ||
| const char CONTACT[30] = "[email protected]"; | ||
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| const struct option mini_tandem_opt [] = { | ||
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@@ -85,7 +85,7 @@ static int usage(void) | |
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| err_printf(" Tandem repeat criteria:\n"); | ||
| // TODO min_copy < 2 ??? | ||
| err_printf(" -c --min-copy INT minimum copy number of tandem repeat [%d]\n", MIN_COPY); | ||
| err_printf(" -c --min-copy INT minimum copy number of tandem repeat (>=%d) [%d]\n", MIN_COPY, MIN_COPY); | ||
| err_printf(" -e --max-diverg INT maximum allowed divergence rate between two consecutive repeats [%.2f]\n", MAX_DIV); | ||
| err_printf(" -p --min-period INT minimum period size of tandem repeat (>=%u) [%u]\n", MIN_PERIOD, DEF_MIN_PERIOD); | ||
| err_printf(" -P --max-period INT maximum period size of tandem repeat (<=%u) [%s]\n", MAX_PERIOD, DEF_MAX_PERIOD_STR); | ||
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@@ -118,7 +118,11 @@ static int usage(void) | |
| err_printf(" if \e[4mr\e[0m is integer: \e[4mR\e[0m = \e[4mr\e[0m\n"); | ||
| err_printf(" -u --unit-seq only output unit sequences of each tandem repeat, no consensus sequence [False]\n"); | ||
| err_printf(" -l --longest only output consensus sequence of tandem repeat that covers the longest read sequence [False]\n"); | ||
| err_printf(" -F --full-len only output full-length consensus sequence [False]\n"); | ||
| err_printf(" -F --full-len only output full-length consensus sequence. [False]\n"); | ||
| err_printf(" full-length: consensus sequence contains both 5' and 3' adapter sequence\n"); | ||
| err_printf(" *Note* only effective when -5 and -3 are provided.\n"); | ||
| err_printf(" -s --single-copy output additional single-copy full-length consensus sequence. [False]\n"); | ||
| err_printf(" *Note* only effective when -F is set and -5 and -3 are provided.\n"); | ||
| err_printf(" -f --out-fmt INT output format [%d]\n", FASTA_FMT); | ||
| err_printf(" - %d: FASTA\n", FASTA_FMT); | ||
| err_printf(" - %d: Tabular\n", TAB_FMT); | ||
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@@ -350,6 +354,7 @@ mini_tandem_para *mini_tandem_init_para(void) { | |
| mtp->only_unit = 0; | ||
| mtp->only_longest = 0; | ||
| mtp->only_full_length = 0; | ||
| mtp->single_copy = 0; | ||
| mtp->out_fmt = FASTA_FMT; | ||
| mtp->detail_fp = NULL; | ||
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@@ -451,7 +456,12 @@ int main(int argc, char *argv[]) | |
| // case 's': mtp->s = atoi(optarg); break; | ||
| case 'H': mtp->hpc = 1; break; | ||
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| case 'c': mtp->min_copy = atoi(optarg); break; | ||
| case 'c': mtp->min_copy = atoi(optarg); | ||
| if (mtp->min_copy < MIN_COPY) { | ||
| err_printf("Error: -c --min-copy needs to be >= %d. (%d)\n", MIN_COPY, mtp->min_copy); | ||
| goto End; | ||
| } | ||
| break; | ||
| case 'e': mtp->max_div = atof(optarg); break; | ||
| case 'p': mtp->min_p = th_parse_num(optarg); | ||
| if (mtp->min_p < MIN_PERIOD) { | ||
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@@ -486,6 +496,7 @@ int main(int argc, char *argv[]) | |
| case 'u': mtp->only_unit = 1; break; | ||
| case 'l': mtp->only_longest = 1; break; | ||
| case 'F': mtp->only_full_length = 1; break; | ||
| case 's': mtp->single_copy = 1; break; | ||
| case 'f': mtp->out_fmt = atoi(optarg); | ||
| if (mtp->out_fmt != FASTA_FMT && mtp->out_fmt != TAB_FMT && mtp->out_fmt != FASTQ_FMT && mtp->out_fmt != TAB_QUAL_FMT) { | ||
| err_printf("\n[main] Error: unknown format number. (-%c)\n", c); | ||
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