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r524: reverted to bwa-mem end bonus 

and reduced the cost of clipping when filtering by identity
This commit is contained in:
Heng Li 2017-10-20 16:57:31 -04:00
parent 15ed0712c2
commit bd04372873
4 changed files with 9 additions and 5 deletions
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4
hit.c
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@ -286,7 +286,7 @@ void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden
mm_reg1_t *r = &regs[(int32_t)aux[i]]; mm_reg1_t *r = &regs[(int32_t)aux[i]];
if (r->qs > en) { if (r->qs > en) {
for (j = en; j < r->qs; ++j) for (j = en; j < r->qs; ++j)
n_diff += qual == 0 || qual[j] >= 53? 0.5f : 0.025f * (qual[j] - 33); n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
blen += r->qs - en; blen += r->qs - en;
} }
assert(r->p); assert(r->p);
@ -295,7 +295,7 @@ void mm_filter_by_identity(void *km, int n_regs, mm_reg1_t *regs, float min_iden
en = en > r->qe? en : r->qe; en = en > r->qe? en : r->qe;
} }
for (j = en; j < qlen; ++j) for (j = en; j < qlen; ++j)
n_diff += qual == 0 || qual[j] >= 53? 0.5f : 0.025f * (qual[j] - 33); n_diff += qual == 0 || qual[j] >= 53? .25f : .05f * .25f * (qual[j] - 33);
blen += qlen - en; blen += qlen - en;
kfree(km, aux); kfree(km, aux);
if (1.0f - n_diff / blen < min_iden) if (1.0f - n_diff / blen < min_iden)

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.2-r523-dirty" #define MM_VERSION "2.2-r524-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

2
map.c
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@ -85,7 +85,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->pe_ori = 0<<1|1; // FR mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1; mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
mo->zdrop = 100; mo->zdrop = 100;
mo->end_bonus = 15; mo->end_bonus = 10;
mo->max_frag_len = 800; mo->max_frag_len = 800;
mo->max_gap = 100; mo->max_gap = 100;
mo->bw = 100; mo->bw = 100;

6
tex/minimap2.tex
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@ -512,7 +512,11 @@ We evaluated minimap2 along with Bowtie2~\citep{Langmead:2012fk}, BWA-MEM and
SNAP~\citep{Zaharia:2011aa}. Minimap2 is 3--4 times as fast as Bowtie2 and SNAP~\citep{Zaharia:2011aa}. Minimap2 is 3--4 times as fast as Bowtie2 and
BWA-MEM, but is 1.3 times slower than SNAP. Minimap2 is more accurate on this BWA-MEM, but is 1.3 times slower than SNAP. Minimap2 is more accurate on this
simulated data set than Bowtie2 and SNAP but less accurate than BWA-MEM simulated data set than Bowtie2 and SNAP but less accurate than BWA-MEM
(Fig.~\ref{fig:eval}b). (Fig.~\ref{fig:eval}b). Closer investigation reveals that BWA-MEM achieves
a higher accuracy partly because it tries to locally align a read in a small
region close to its mate. If we disable this feature, BWA-MEM becomes slightly
less accurate than minimap2. We might consider to implement a similar heuristic
in minimap2 in future.
\section{Conclusion} \section{Conclusion}