X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_rmdup.c.pysam.c;fp=samtools%2Fbam_rmdup.c.pysam.c;h=2d5a718673f232a8b37615e78065f6c5d8032d73;hp=0000000000000000000000000000000000000000;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089 diff --git a/samtools/bam_rmdup.c.pysam.c b/samtools/bam_rmdup.c.pysam.c new file mode 100644 index 0000000..2d5a718 --- /dev/null +++ b/samtools/bam_rmdup.c.pysam.c @@ -0,0 +1,208 @@ +#include "pysam.h" + +#include +#include +#include +#include +#include +#include "sam.h" + +typedef bam1_t *bam1_p; + +#include "khash.h" +KHASH_SET_INIT_STR(name) +KHASH_MAP_INIT_INT64(pos, bam1_p) + +#define BUFFER_SIZE 0x40000 + +typedef struct { + uint64_t n_checked, n_removed; + khash_t(pos) *best_hash; +} lib_aux_t; +KHASH_MAP_INIT_STR(lib, lib_aux_t) + +typedef struct { + int n, max; + bam1_t **a; +} tmp_stack_t; + +static inline void stack_insert(tmp_stack_t *stack, bam1_t *b) +{ + if (stack->n == stack->max) { + stack->max = stack->max? stack->max<<1 : 0x10000; + stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max); + } + stack->a[stack->n++] = b; +} + +static inline void dump_best(tmp_stack_t *stack, samfile_t *out) +{ + int i; + for (i = 0; i != stack->n; ++i) { + samwrite(out, stack->a[i]); + bam_destroy1(stack->a[i]); + } + stack->n = 0; +} + +static void clear_del_set(khash_t(name) *del_set) +{ + khint_t k; + for (k = kh_begin(del_set); k < kh_end(del_set); ++k) + if (kh_exist(del_set, k)) + free((char*)kh_key(del_set, k)); + kh_clear(name, del_set); +} + +static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) +{ + khint_t k = kh_get(lib, aux, lib); + if (k == kh_end(aux)) { + int ret; + char *p = strdup(lib); + lib_aux_t *q; + k = kh_put(lib, aux, p, &ret); + q = &kh_val(aux, k); + q->n_checked = q->n_removed = 0; + q->best_hash = kh_init(pos); + return q; + } else return &kh_val(aux, k); +} + +static void clear_best(khash_t(lib) *aux, int max) +{ + khint_t k; + for (k = kh_begin(aux); k != kh_end(aux); ++k) { + if (kh_exist(aux, k)) { + lib_aux_t *q = &kh_val(aux, k); + if (kh_size(q->best_hash) >= max) + kh_clear(pos, q->best_hash); + } + } +} + +static inline int sum_qual(const bam1_t *b) +{ + int i, q; + uint8_t *qual = bam1_qual(b); + for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; + return q; +} + +void bam_rmdup_core(samfile_t *in, samfile_t *out) +{ + bam1_t *b; + int last_tid = -1, last_pos = -1; + tmp_stack_t stack; + khint_t k; + khash_t(lib) *aux; + khash_t(name) *del_set; + + aux = kh_init(lib); + del_set = kh_init(name); + b = bam_init1(); + memset(&stack, 0, sizeof(tmp_stack_t)); + + kh_resize(name, del_set, 4 * BUFFER_SIZE); + while (samread(in, b) >= 0) { + bam1_core_t *c = &b->core; + if (c->tid != last_tid || last_pos != c->pos) { + dump_best(&stack, out); // write the result + clear_best(aux, BUFFER_SIZE); + if (c->tid != last_tid) { + clear_best(aux, 0); + if (kh_size(del_set)) { // check + fprintf(pysamerr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set)); + clear_del_set(del_set); + } + if ((int)c->tid == -1) { // append unmapped reads + samwrite(out, b); + while (samread(in, b) >= 0) samwrite(out, b); + break; + } + last_tid = c->tid; + fprintf(pysamerr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]); + } + } + if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) { + samwrite(out, b); + } else if (c->isize > 0) { // paired, head + uint64_t key = (uint64_t)c->pos<<32 | c->isize; + const char *lib; + lib_aux_t *q; + int ret; + lib = bam_get_library(in->header, b); + q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); + ++q->n_checked; + k = kh_put(pos, q->best_hash, key, &ret); + if (ret == 0) { // found in best_hash + bam1_t *p = kh_val(q->best_hash, k); + ++q->n_removed; + if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle + kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed + bam_copy1(p, b); // replaced as b + } else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed + if (ret == 0) + fprintf(pysamerr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b)); + } else { // not found in best_hash + kh_val(q->best_hash, k) = bam_dup1(b); + stack_insert(&stack, kh_val(q->best_hash, k)); + } + } else { // paired, tail + k = kh_get(name, del_set, bam1_qname(b)); + if (k != kh_end(del_set)) { + free((char*)kh_key(del_set, k)); + kh_del(name, del_set, k); + } else samwrite(out, b); + } + last_pos = c->pos; + } + + for (k = kh_begin(aux); k != kh_end(aux); ++k) { + if (kh_exist(aux, k)) { + lib_aux_t *q = &kh_val(aux, k); + dump_best(&stack, out); + fprintf(pysamerr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, + (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); + kh_destroy(pos, q->best_hash); + free((char*)kh_key(aux, k)); + } + } + kh_destroy(lib, aux); + + clear_del_set(del_set); + kh_destroy(name, del_set); + free(stack.a); + bam_destroy1(b); +} + +void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se); + +int bam_rmdup(int argc, char *argv[]) +{ + int c, is_se = 0, force_se = 0; + samfile_t *in, *out; + while ((c = getopt(argc, argv, "sS")) >= 0) { + switch (c) { + case 's': is_se = 1; break; + case 'S': force_se = is_se = 1; break; + } + } + if (optind + 2 > argc) { + fprintf(pysamerr, "\n"); + fprintf(pysamerr, "Usage: samtools rmdup [-sS] \n\n"); + fprintf(pysamerr, "Option: -s rmdup for SE reads\n"); + fprintf(pysamerr, " -S treat PE reads as SE in rmdup (force -s)\n\n"); + return 1; + } + in = samopen(argv[optind], "rb", 0); + out = samopen(argv[optind+1], "wb", in->header); + if (in == 0 || out == 0) { + fprintf(pysamerr, "[bam_rmdup] fail to read/write input files\n"); + return 1; + } + if (is_se) bam_rmdupse_core(in, out, force_se); + else bam_rmdup_core(in, out); + samclose(in); samclose(out); + return 0; +}