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-q option to put seq/qual strings in secondary alignments #36

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-q option to put seq/qual strings in secondary alignments #36

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2 changes: 1 addition & 1 deletion bwamem.c
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Original file line number Diff line number Diff line change
Expand Up @@ -869,7 +869,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
kputc('\t', str);

// print SEQ and QUAL
if (p->flag & 0x100) { // for secondary alignments, don't write SEQ and QUAL
if ((p->flag & 0x100) && !(opt->flag&MEM_F_SEC_SEQ_QUAL)) { // for secondary alignments, don't write SEQ and QUAL unless told to
kputsn("*\t*", 3, str);
} else if (!p->is_rev) { // the forward strand
int i, qb = 0, qe = s->l_seq;
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20 changes: 10 additions & 10 deletions bwamem.h
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Expand Up @@ -11,16 +11,16 @@
struct __smem_i;
typedef struct __smem_i smem_i;

#define MEM_F_PE 0x2
#define MEM_F_NOPAIRING 0x4
#define MEM_F_ALL 0x8
#define MEM_F_NO_MULTI 0x10
#define MEM_F_NO_RESCUE 0x20
#define MEM_F_SELF_OVLP 0x40
#define MEM_F_ALN_REG 0x80
#define MEM_F_REF_HDR 0x100
#define MEM_F_SOFTCLIP 0x200

#define MEM_F_PE 0x2
#define MEM_F_NOPAIRING 0x4
#define MEM_F_ALL 0x8
#define MEM_F_NO_MULTI 0x10
#define MEM_F_NO_RESCUE 0x20
#define MEM_F_SELF_OVLP 0x40
#define MEM_F_ALN_REG 0x80
#define MEM_F_REF_HDR 0x100
#define MEM_F_SOFTCLIP 0x200
#define MEM_F_SEC_SEQ_QUAL 0x400
typedef struct {
int a, b; // match score and mismatch penalty
int o_del, e_del;
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4 changes: 3 additions & 1 deletion fastmap.c
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Expand Up @@ -55,7 +55,7 @@ int main_mem(int argc, char *argv[])

opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "epaFMCSPHVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
while ((c = getopt(argc, argv, "epaFMCSPHVYjkq:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == 'x') mode = optarg;
else if (c == 'w') opt->w = atoi(optarg), opt0.w = 1;
Expand All @@ -73,6 +73,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'F') opt->flag |= MEM_F_ALN_REG;
else if (c == 'Y') opt->flag |= MEM_F_SOFTCLIP;
else if (c == 'V') opt->flag |= MEM_F_REF_HDR;
else if (c == 'q') opt->flag |= MEM_F_SEC_SEQ_QUAL;
else if (c == 'c') opt->max_occ = atoi(optarg), opt0.max_occ = 1;
else if (c == 'd') opt->zdrop = atoi(optarg), opt0.zdrop = 1;
else if (c == 'v') bwa_verbose = atoi(optarg);
Expand Down Expand Up @@ -174,6 +175,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -T INT minimum score to output [%d]\n", opt->T);
fprintf(stderr, " -h INT[,INT] if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", opt->max_XA_hits, opt->max_XA_hits_alt);
fprintf(stderr, " -a output all alignments for SE or unpaired PE\n");
fprintf(stderr, " -q write seq/qual strings for secondary alignments\n");
fprintf(stderr, " -C append FASTA/FASTQ comment to SAM output\n");
fprintf(stderr, " -V output the reference FASTA header in the XR tag\n");
fprintf(stderr, " -Y use soft clipping for supplementary alignments\n");
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