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rerelease v0.13

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chhylp123
2020-10-22 14:24:59 -04:00
parent de4163e881
commit b2b4624cea
4 changed files with 8 additions and 6 deletions
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CommandLines.cpp
+3 -3
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@@ -24,7 +24,7 @@ static ko_longopt_t long_options[] = {
{ "purge-cov", ko_required_argument, 309 }, { "purge-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 }, { "pri-range", ko_required_argument, 310 },
{ "high-het", ko_no_argument, 311 }, { "high-het", ko_no_argument, 311 },
{ "pb-range", ko_required_argument, 312 }, { "lowQ", ko_required_argument, 312 },
{ 0, 0, 0 } { 0, 0, 0 }
}; };
@@ -60,7 +60,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate); fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate); fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -u disable post join contigs step which may improve N50\n"); fprintf(stderr, " -u disable post join contigs step which may improve N50\n");
fprintf(stderr, " --pb-range INT\n"); fprintf(stderr, " --lowQ INT\n");
fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate); fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate);
// fprintf(stderr, " --pri-range INT1[,INT2]\n"); // fprintf(stderr, " --pri-range INT1[,INT2]\n");
// fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n"); // fprintf(stderr, " keep contigs with coverage in this range in p_ctg.gfa; -1 to disable [auto,inf]\n");
@@ -133,7 +133,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_min = -1024; asm_opt->recover_atg_cov_min = -1024;
asm_opt->recover_atg_cov_max = INT_MAX; asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1; asm_opt->hom_global_coverage = -1;
asm_opt->bed_inconsist_rate = 0; asm_opt->bed_inconsist_rate = 70;
} }
void destory_opt(hifiasm_opt_t* asm_opt) void destory_opt(hifiasm_opt_t* asm_opt)
CommandLines.h
+1 -1
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@@ -3,7 +3,7 @@
#include <pthread.h> #include <pthread.h>
#define HA_VERSION "0.13-r307" #define HA_VERSION "0.13-r308"
#define VERBOSE 0 #define VERBOSE 0
Overlaps.cpp
+2
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@@ -27472,6 +27472,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
*coverage_cut_ptr = coverage_cut; *coverage_cut_ptr = coverage_cut;
*sg_ptr = sg; *sg_ptr = sg;
fprintf(stderr, "Inconsistency threshold for low-quality regions in BED files: %u%%\n", asm_opt.bed_inconsist_rate);
} }
void build_string_graph_without_clean( void build_string_graph_without_clean(
hifiasm.1
+2 -2
View File
@@ -201,11 +201,11 @@ If INT2 is not specified, it is set to infinity.
Set -1 to disable. Set -1 to disable.
.TP .TP
.BI --pb-range \ INT .BI --lowQ \ INT
Output contig regions with >=INT% inconsistency to the bed file Output contig regions with >=INT% inconsistency to the bed file
with suffix with suffix
.B lowQ.bed .B lowQ.bed
[0]. Set 0 to disable. [70]. Set 0 to disable.
.SS Trio-partition options .SS Trio-partition options