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r229: a new way to prevent out-of-band backtrack

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Heng Li
2017-07-29 23:52:30 -04:00
parent fa99d28d34
commit 5934d68772
7 changed files with 47 additions and 61 deletions
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main.c
+3 -1
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@@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r228-dirty"
#define MM_VERSION "2.0-r229-dirty"
void liftrlimit()
{
@@ -30,6 +30,7 @@ static struct option long_options[] = {
{ "print-seed", no_argument, 0, 0 },
{ "max-chain-skip", required_argument, 0, 0 },
{ "min-dp-len", required_argument, 0, 0 },
{ "print-aln-seq", no_argument, 0, 0 },
{ "version", no_argument, 0, 'V' },
{ "min-count", required_argument, 0, 'n' },
{ "min-chain-score",required_argument, 0, 'm' },
@@ -85,6 +86,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED; // --print-seed
else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip
else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ; // --print-aln-seq
else if (c == 'V') {
puts(MM_VERSION);
return 0;