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r985: optionally report cs/cg on the query strand

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PAF only; not well tested
This commit is contained in:
Heng Li
2020-04-21 12:37:35 -04:00
parent 29f67a1666
commit da7109fd29
9 changed files with 114 additions and 42 deletions
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main.c
+3 -1
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r974-dirty"
#define MM_VERSION "2.17-r985-qs-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -70,6 +70,7 @@ static ko_longopt_t long_options[] = {
{ "chain-gap-scale",ko_required_argument, 343 },
{ "alt", ko_required_argument, 344 },
{ "alt-drop", ko_required_argument, 345 },
{ "qstrand", ko_no_argument, 346 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
{ "version", ko_no_argument, 'V' },
@@ -217,6 +218,7 @@ int main(int argc, char *argv[])
else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
else if (c == 344) alt_list = o.arg; // --alt
else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
else if (c == 346) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
else if (c == 314) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
} else if (c == 315) { // --secondary