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r211: added --write-paf/--write-ec/--skip-triobin

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Heng Li
2020-04-08 22:32:54 -04:00
parent 23dbfdef77
commit c41aae0630
8 changed files with 32 additions and 24 deletions
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10
Assembly.cpp
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@@ -1156,11 +1156,13 @@ int ha_assemble(void)
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());
trio_partition();
if (!(asm_opt.flag & HA_F_SKIP_TRIOBIN)) trio_partition();
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
}
if (!ovlp_loaded) {
// construct hash table for high occurrence k-mers
if (!asm_opt.no_kmer_flt) {
if (!(asm_opt.flag & HA_F_NO_KMER_FLT)) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov);
ha_opt_update_cov(&asm_opt, hom_cov);
}
@@ -1175,7 +1177,7 @@ int ha_assemble(void)
asm_opt.num_bases, asm_opt.num_corrected_bases, asm_opt.num_recorrected_bases);
fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
}
//Output_corrected_reads();
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> written corrected reads to disk\n", __func__, yak_realtime(), yak_cpu_usage());
// overlap between corrected reads
ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
@@ -1184,7 +1186,7 @@ int ha_assemble(void)
yak_cpu_usage(), yak_peakrss_in_gb());
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
//Output_PAF();
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
trio_partition();
}
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,