From a531a4cbdac228182c6e2a271537423ceae86340 Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Sun, 27 Jun 2021 07:48:29 -0400 Subject: [PATCH] debugging for huge datasets --- CommandLines.h | 2 +- Overlaps.cpp | 11 ++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/CommandLines.h b/CommandLines.h index 67d13a6..e7b9b1c 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -4,7 +4,7 @@ #include #include -#define HA_VERSION "0.15.4-r343" +#define HA_VERSION "0.15.4-r347" #define VERBOSE 0 diff --git a/Overlaps.cpp b/Overlaps.cpp index 57f8a23..300929c 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -16009,8 +16009,9 @@ asg_t* copy_read_graph(asg_t *src) dest->is_srt = src->is_srt; dest->is_symm = src->is_symm; - dest->idx = (uint64_t*)malloc(dest->n_seq*2*8); - memcpy(dest->idx, src->idx, dest->n_seq*2*8); + dest->idx = NULL; + // dest->idx = (uint64_t*)malloc(dest->n_seq*2*8); + // memcpy(dest->idx, src->idx, dest->n_seq*2*8); asg_cleanup(dest); if(src->seq_vis) @@ -30961,7 +30962,7 @@ 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); - + set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, max_hang_length, mini_overlap_length); @@ -30971,7 +30972,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) output_unitig_graph(sg, coverage_cut, o_file, sources, ruIndex, max_hang_length, mini_overlap_length); // flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL; flat_soma_v(sg, sources, ruIndex); free(ruIndex->is_het); ruIndex->is_het = NULL; - + output_contig_graph_primary_pre(sg, coverage_cut, o_file, sources, reverse_sources, asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length); @@ -30981,7 +30982,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g) debug_gfa:; set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, max_hang_length, mini_overlap_length); } - + if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt)) { if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;