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r1069: fixed a regression in comparison to v2.18 

for PE short reads. An interesting omission. Resolves #776
This commit is contained in:
Heng Li 2021-07-02 11:45:21 -04:00
parent e6cce019e4
commit 459ce04c84
2 changed files with 4 additions and 3 deletions
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5
lchain.c
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@ -114,8 +114,9 @@ static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t ma
float lin_pen, log_pen;
lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg;
log_pen = dd >= 1? mg_log2(dd + 1) : 0.0f; // mg_log2() only works for dd>=2
if (is_cdna) {
if (dr > dq) sc -= (int)(lin_pen < log_pen? lin_pen : log_pen); // deletion or jump between paired ends
if (is_cdna || sidi != sidj) {
if (sidi != sidj && dr == 0) ++sc; // possibly due to overlapping paired ends; give a minor bonus
else if (dr > dq || sidi != sidj) sc -= (int)(lin_pen < log_pen? lin_pen : log_pen); // deletion or jump between paired ends
else sc -= (int)(lin_pen + .5f * log_pen);
} else sc -= (int)(lin_pen + .5f * log_pen);
}

2
main.c
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@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.20-r1068-dirty"
#define MM_VERSION "2.20-r1069-dirty"
#ifdef __linux__
#include <sys/resource.h>