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r539: use --splice-flank=yes by default 

In human/mouse, the GTr..yAG pattern occurs to 91/92% of all GT-AG introns.
Modeling r..y clearly leads to higher accuracy. However, in SIRV, this
percentage is reduced to ~60%. The default "--splice --splice-flank=yes"
leads to lower accuracy. If someone benchmark minimap2 on SIRV, this would be
bad, but minimap2 is developed for practical applications, not for benchmarks.
I will live with that.
This commit is contained in:
Heng Li 2017-10-28 22:29:55 -04:00
parent f22a94e868
commit 192217a10c
3 changed files with 27 additions and 7 deletions
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2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.3-r538-dirty" #define MM_VERSION "2.3-r539-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>

2
map.c
View File

@ -105,7 +105,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->mini_batch_size = 50000000; mo->mini_batch_size = 50000000;
} else if (strcmp(preset, "splice") == 0 || strcmp(preset, "cdna") == 0) { } else if (strcmp(preset, "splice") == 0 || strcmp(preset, "cdna") == 0) {
io->is_hpc = 0, io->k = 15, io->w = 5; io->is_hpc = 0, io->k = 15, io->w = 5;
mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV; mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000; mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000;
mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0; mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
mo->noncan = 9; mo->noncan = 9;

30
minimap2.1
View File

@ -220,7 +220,9 @@ costs
In the splice mode, the second gap penalties are not used. In the splice mode, the second gap penalties are not used.
.TP .TP
.BI -C \ INT .BI -C \ INT
Cost for a non-canonical GT-AG splicing [0] Cost for a non-canonical GT-AG splicing (effective with
.BR --splice )
[0]
.TP .TP
.BI -z \ INT .BI -z \ INT
Break an alignment if the running score drops too quickly along the diagonal of Break an alignment if the running score drops too quickly along the diagonal of
@ -243,7 +245,25 @@ both strands;
no attempt to match GT-AG [n] no attempt to match GT-AG [n]
.TP .TP
.BI --end-bonus \ INT .BI --end-bonus \ INT
Score bonus when alignment extends to the end of the query sequence [10]. Score bonus when alignment extends to the end of the query sequence [0].
.TP
.BR --splice-flank [= yes | no ]
Assume the next base to a
.B GT
donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
base to a
.B AG
acceptor tends to be C/T [yes with
.BR --splice ].
This trend is evolutionarily conservative, all the way to S. cerevisiae
(PMID:18688272). Specifying this option generally leads to higher junction
accuracy by several percents, so it is applied by default with
.BR --splice .
However, the SIRV control does not honor this trend
(only ~60%). This option reduces accuracy. If you are benchmarking minimap2
on SIRV data, please add
.B --splice-flank=no
to the command line.
.SS Input/output options .SS Input/output options
.TP 10 .TP 10
.B -a .B -a
@ -261,7 +281,7 @@ the real CIGAR in memory.
.TP .TP
.BI -R \ STR .BI -R \ STR
SAM read group line in a format like SAM read group line in a format like
.RB @RG\\\\tID:foo\\\\tSM:bar .B @RG\\\\tID:foo\\\\tSM:bar
[]. [].
.TP .TP
.B -c .B -c
@ -371,8 +391,8 @@ is that this preset is not using HPC minimizers.
.B splice .B splice
Long-read spliced alignment Long-read spliced alignment
.RB ( -k15 .RB ( -k15
.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 .B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub
.BR -ub ). .BR --splice-flank=yes ).
In the splice mode, 1) long deletions are taken as introns and represented as In the splice mode, 1) long deletions are taken as introns and represented as
the the
.RB ` N ' .RB ` N '