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r784: support the =/X CIGAR operators (#156)

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This commit is contained in:
Heng Li
2018-05-30 16:11:22 -04:00
parent a3afeec0b2
commit 154d2caf5b
5 changed files with 81 additions and 4 deletions
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main.c
+4 -1
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@@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r783-dirty"
#define MM_VERSION "2.10-r784-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -59,6 +59,7 @@ static struct option long_options[] = {
{ "MD", no_argument, 0, 0 }, // 29
{ "lj-min-ratio", required_argument, 0, 0 }, // 30
{ "score-N", required_argument, 0, 0 }, // 31
{ "eqx", no_argument, 0, 0 }, // 32
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -177,6 +178,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==29) opt.flag |= MM_F_OUT_MD; // --MD
else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary
@@ -278,6 +280,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -c output CIGAR in PAF\n");
fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none]\n");
fprintf(fp_help, " --MD output the MD tag\n");
fprintf(fp_help, " --eqx write =/X CIGAR operators\n");
fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n");