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r475: added --cs=none; updated manpage

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Heng Li
2017-10-05 15:27:37 -04:00
parent f4a5d3a692
commit b839758335
2 changed files with 42 additions and 6 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-r474-dirty"
#define MM_VERSION "2.2-r475-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -143,6 +143,8 @@ int main(int argc, char *argv[])
opt.flag &= ~MM_F_OUT_CS_LONG;
} else if (strcmp(optarg, "long") == 0) {
opt.flag |= MM_F_OUT_CS_LONG;
} else if (strcmp(optarg, "none") == 0) {
opt.flag &= ~MM_F_OUT_CS;
} else if (mm_verbose >= 2) {
fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
}
@@ -222,7 +224,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -Q don't output base quality in SAM\n");
fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
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' [no cs]\n");
fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none]\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [200M]\n");
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);