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r254: added --ex-list and --ex-iter

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Heng Li
2020-06-03 20:46:34 -04:00
parent e247c5f042
commit eddbc61952
6 changed files with 192 additions and 4 deletions
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5
Assembly.cpp
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@@ -1159,10 +1159,15 @@ void ha_overlap_final(void)
int ha_assemble(void)
{
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r, hom_cov = -1, ovlp_loaded = 0;
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
if (asm_opt.extract_list) {
ha_extract_print_list(&R_INF, asm_opt.extract_iter, asm_opt.extract_list);
exit(0);
}
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN) && !(asm_opt.flag & HA_F_VERBOSE_GFA)) ha_triobin(&asm_opt);
///if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) ha_triobin(&asm_opt);
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();