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increase maximum barcode length limit to 63bp

This commit is contained in:
Heng Li 2011-06-09 17:17:13 -04:00
parent 243e735431
commit a74523a68d
3 changed files with 6 additions and 4 deletions
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4
bwaseqio.c
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@ -149,8 +149,8 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24; int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
long n_trimmed = 0, n_tot = 0; long n_trimmed = 0, n_tot = 0;
if (l_bc > 15) { if (l_bc > BWA_MAX_BCLEN) {
fprintf(stderr, "[%s] the maximum barcode length is 15.\n", __func__); fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
return 0; return 0;
} }
if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input

4
bwtaln.h
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@ -22,6 +22,8 @@
#define BWA_AVG_ERR 0.02 #define BWA_AVG_ERR 0.02
#define BWA_MIN_RDLEN 35 // for read trimming #define BWA_MIN_RDLEN 35 // for read trimming
#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
#ifndef bns_pac #ifndef bns_pac
#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3) #define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
#endif #endif
@ -75,7 +77,7 @@ typedef struct {
// for multi-threading only // for multi-threading only
int tid; int tid;
// barcode // barcode
char bc[16]; // null terminated; up to 15 bases char bc[BWA_MAX_BCLEN+1]; // null terminated; up to BWA_MAX_BCLEN bases
// NM and MD tags // NM and MD tags
uint32_t full_len:20, nm:12; uint32_t full_len:20, nm:12;
char *md; char *md;

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.5.9-r18-dev" #define PACKAGE_VERSION "0.5.9-r19-dev"
#endif #endif
static int usage() static int usage()