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debugging for huge datasets

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chhylp123
2021-06-27 07:48:29 -04:00
parent 0410662841
commit a531a4cbda
2 changed files with 7 additions and 6 deletions
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CommandLines.h
+1 -1
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@@ -4,7 +4,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.15.4-r343" #define HA_VERSION "0.15.4-r347"
#define VERBOSE 0 #define VERBOSE 0
Overlaps.cpp
+6 -5
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@@ -16009,8 +16009,9 @@ asg_t* copy_read_graph(asg_t *src)
dest->is_srt = src->is_srt; dest->is_srt = src->is_srt;
dest->is_symm = src->is_symm; dest->is_symm = src->is_symm;
dest->idx = (uint64_t*)malloc(dest->n_seq*2*8); dest->idx = NULL;
memcpy(dest->idx, src->idx, dest->n_seq*2*8); // dest->idx = (uint64_t*)malloc(dest->n_seq*2*8);
// memcpy(dest->idx, src->idx, dest->n_seq*2*8);
asg_cleanup(dest); asg_cleanup(dest);
if(src->seq_vis) 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, // rescue_no_coverage_aggressive(sg, sources, reverse_sources, &coverage_cut, ruIndex, max_hang_length,
// mini_overlap_length, bubble_dist, 10); // mini_overlap_length, bubble_dist, 10);
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex,
max_hang_length, mini_overlap_length); 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); 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_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; 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, 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); 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:; debug_gfa:;
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex, max_hang_length, mini_overlap_length); 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 (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{ {
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION; if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;