From e6e6dbf7b3cbec0b0165800d4c94bfc9a72ab2b6 Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Thu, 18 Mar 2021 13:44:30 -0400 Subject: [PATCH] remove unnecessary bin files of Hi-C --- CommandLines.h | 2 +- Overlaps.cpp | 12 +++++------- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/CommandLines.h b/CommandLines.h index 8616112..a6b0924 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -3,7 +3,7 @@ #include -#define HA_VERSION "0.14.1-r313" +#define HA_VERSION "0.14.1-r314" #define VERBOSE 0 diff --git a/Overlaps.cpp b/Overlaps.cpp index 2d9782c..f55819d 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -11964,7 +11964,7 @@ bub_label_t* b_mask_t) hc_links link; - if(load_hc_links(&link, output_file_name) == 0) + ///if(load_hc_links(&link, output_file_name) == 0) { init_hc_links(&link, ug->g->n_seq, R_INF.total_reads); asg_t *copy_sg = copy_read_graph(sg); @@ -11980,7 +11980,7 @@ bub_label_t* b_mask_t) ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, &link); - write_hc_links(&link, output_file_name); + ///write_hc_links(&link, output_file_name); } @@ -28169,6 +28169,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g) // rescue_no_coverage_aggressive(sg, sources, reverse_sources, &coverage_cut, ruIndex, max_hang_length, // mini_overlap_length, bubble_dist, 10); + rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, + ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz, &b_mask_t); if (asm_opt.flag & HA_F_VERBOSE_GFA) { @@ -28177,11 +28179,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) debug_gfa:; /*******************************for debug***************************************/ } - - rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, - ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz, &b_mask_t); - - + if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt)) { char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);