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r512: option to filter poorly aligned reads

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This commit is contained in:
Heng Li
2017-10-16 10:38:22 -04:00
parent 858213d513
commit e6f525edaf
8 changed files with 131 additions and 38 deletions
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main.c
+4 -2
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r511-dirty"
#define MM_VERSION "2.2-r512-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -65,7 +65,7 @@ static inline int64_t mm_parse_num(const char *str)
int main(int argc, char *argv[])
{
const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:";
const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:i:";
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, long_idx, max_gap_ref = 0;
@@ -100,6 +100,7 @@ int main(int argc, char *argv[])
else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
else if (c == 'G') max_gap_ref = (int)mm_parse_num(optarg);
else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
else if (c == 'i') opt.min_iden = atof(optarg);
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
@@ -222,6 +223,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(fp_help, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
fprintf(fp_help, " -i FLOAT min identity (mapQ reduced to 0 if below) [0]\n");
fprintf(fp_help, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\n");
fprintf(fp_help, " -Q don't output base quality in SAM\n");