From 20e52f326cdf1b6c2ca9b2c0b5be07637d9196d2 Mon Sep 17 00:00:00 2001 From: flu0r1ne Date: Sun, 30 Oct 2022 19:30:29 -0500 Subject: Initial commit --- main.c | 928 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 928 insertions(+) create mode 100644 main.c (limited to 'main.c') diff --git a/main.c b/main.c new file mode 100644 index 0000000..aa2f3d6 --- /dev/null +++ b/main.c @@ -0,0 +1,928 @@ +#include +#include +#include +#include +#include +#include +#include +#include + +#include "util/sds/sds.h" +#include "util/prime_search.h" +#include "util/hash.h" +#include "util/util.h" + +#include + +// @abstract Structure representing an unique alignment and virtual file pointer +// @field tid chromosome ID +// @field pos 0-based leftmost coordinate +// @field vptr virtual pointer +typedef struct { + uint32_t tid; + uint32_t pos; + uint64_t vptr; +} aln_spec_t; + + +#pragma pack(push, 1) + +typedef struct { + uint32_t tid; + uint32_t pos; + uint64_t vptr; +} aln_spec_packed_t; + +#pragma pack(pop) + +// constrains (qname < 2 ** 32) + +// @abstract Structure representing all alignments by queryname +// @field qname queryname (name for the given read) +// @field n_alns number of alignments +// @field alns array with alignments structures +typedef struct { + char * qname; + uint16_t n_alns; + aln_spec_t * alns; +} qidx_record_t; + +// @abstract Get the marshaled size of a record +static size_t qidx_record_msize(qidx_record_t const * q) { + return ( + strlen(q->qname) + 1 + + sizeof(uint16_t) + + sizeof(aln_spec_packed_t) * q->n_alns + ); +} + +// @abstract Martial a record to a fixed buffer +// +// @param q query index record +// @param dst destination buffer +// @param dstlen length of the destination buffer +// +// @return returns the number of bytes written to the buffer +// or < 0 if the destination buffer is exceeded +ssize_t qidx_record_marital(qidx_record_t const * q, void * dst, size_t dstlen) { + size_t rem = dstlen; + + size_t n = strlen(q->qname) + 1; + if(rem < n) + return -1; + rem -= n; + + { + char * _dst = dst; + strcpy(_dst, q->qname); + dst = (_dst + n); + } + + size_t sz = 0; + sz += sizeof(uint16_t); + sz += sizeof(aln_spec_packed_t) * q->n_alns; + + if(rem < sz) + return -1; + rem -= sz; + + { + uint16_t * _dst = dst; + *_dst = htole16(q->n_alns); + dst = _dst + 1; + } + + aln_spec_packed_t * buf_aln = dst; + for(size_t i = 0; i < q->n_alns; i++) { + aln_spec_t * aln = &q->alns[i]; + + buf_aln->tid = htole32(aln->tid); + buf_aln->pos = htole32(aln->pos); + buf_aln->vptr = htole64(aln->vptr); + + buf_aln++; + } + + return dstlen - rem; +} + +// @abstract Helper to parse the query name and the number of alignments +// @returns NULL if a parsing error occured else the location after the buffer +static void const * _parse_record_header(void const * buf, size_t buflen, + char const ** qname, uint16_t * n_alns) { + + size_t n = strnlen(buf, buflen) + 1; + *qname = buf; + + if(n + sizeof(uint16_t) > buflen) + return NULL; + + uint16_t const * _n_alns = (uint16_t const *) (*qname + n); + *n_alns = le64toh(*_n_alns); + buf = _n_alns + 1; + + if(sizeof(aln_spec_packed_t) * *n_alns > buflen) + return NULL; + + return buf; +} + +// @abstract Unmartial a query record. The resulting memory needs to be freed. +// All strings are sds strings. +// +// @param q query index record +// @param buf source buffer +// @param buflen source buffer length +// +// @return a pointer within buf after the record +// or NULL if a parsing error occurred +void const * qidx_record_unmartial(qidx_record_t * q, void const * buf, size_t buflen) { + char const * qname; + + if(!(buf = _parse_record_header(buf, buflen, &qname, &q->n_alns))) { + return NULL; + } + + q->qname = sdsnew(qname); + q->alns = calloc(q->n_alns, sizeof(aln_spec_t)); + + aln_spec_packed_t const * buf_aln = buf; + for(size_t i = 0; i < q->n_alns; i++) { + aln_spec_t * aln = &q->alns[i]; + + aln->pos = le32toh(buf_aln->pos); + aln->tid = le32toh(buf_aln->tid); + aln->vptr = le64toh(buf_aln->vptr); + + buf_aln++; + } + + return buf_aln; +} + +// @abstract Find a record efficiently in a marshaled buffer of query index records +// +// @param buf source buffer +// @param buflen length of the source buffer +// @param qname target queryname +// +// @returns a pointer to a target query or NULL if it a record with the target query name +// does not exist in the buffer +void const * qidx_record_martial_find(void const * buf, size_t buflen, char const * qname) { + size_t n = strnlen(buf, buflen); + + char const * _qname; + uint16_t n_alns; + + void const * cur = buf, + * next = NULL; + + while((next = _parse_record_header(cur, buflen, &_qname, &n_alns))) { + + if(strcmp(_qname, qname) == 0) { + return cur; + } + + next = (aln_spec_packed_t *) next + n_alns; + size_t l = (char const *) next - (char const *) cur; + buflen -= l; + cur = next; + + if(!buflen) { + return NULL; + } + } + + // Invalid + return NULL; +} + +typedef enum { + QIDX_OK = 0, + QIDX_ITER_DONE, + QIDX_NO_MEM, + QIDX_NO_BAM_HDR, + QIDX_BAM_READ_FAILURE, + QIDX_REC_ITER_FAILURE, + QIDX_NOT_SORTED, + QIDX_BUCKET_MAX_SIZE_EXCEEDED, + QIDX_MAP_FAIL, + QIDX_IO_FAIL, + QIDX_FAILED_TO_OPEN_BAMFILE, + QIDX_FAILED_TO_OPEN_INDEX_FILE, + QIDX_INVALID_VERSION, + QIDX_INVALID_MAGIC, +} qidx_err_t; + +bool qidx_errno(qidx_err_t err) { + switch(err) { + case QIDX_MAP_FAIL: + case QIDX_IO_FAIL: + return true; + default: + return false; + } + +} + +char const * qidx_strerr(qidx_err_t err) { + switch(err) { + case QIDX_NO_MEM: return "memory was exausted"; + case QIDX_NO_BAM_HDR: return "parsing BAM header failed"; + case QIDX_BAM_READ_FAILURE: return "failed to read bamfile"; + case QIDX_REC_ITER_FAILURE: return "bam query index record iterator failed"; + case QIDX_NOT_SORTED: return "input bam file not sorted by query name"; + case QIDX_BUCKET_MAX_SIZE_EXCEEDED: return "maximum query size exceeded"; + case QIDX_MAP_FAIL: return "mmap failed"; + case QIDX_IO_FAIL: return "qidx io failure"; + case QIDX_FAILED_TO_OPEN_BAMFILE: return "failed to open bamfile"; + case QIDX_FAILED_TO_OPEN_INDEX_FILE: return "failed to open indexfile"; + case QIDX_INVALID_MAGIC: return "invalid magic number (not a qidx or corrupted)"; + case QIDX_INVALID_VERSION: return "qidx version outdated, please regenerate"; + case QIDX_ITER_DONE: + case QIDX_OK: + return "OK"; + } +} + +qidx_err_t init_qidx(qidx_record_t * r) { + return QIDX_OK; +} + +void qidx_free(qidx_record_t * r) { + free(r); +} + +/* + * SAMTOOLS SORTING ALGORITHM + */ + +// strnum_cmp is the string comparator used by samtools sort +// to sort bam files by read names (e.g. QNAME) +// +// The input file is expected to be ordered accordingly. This +// is verified at runtime. +#define is_digit(c) ((c)<='9' && (c)>='0') +static int strnum_cmp(const char *_a, const char *_b) +{ + const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b; + const unsigned char *pa = a, *pb = b; + while (*pa && *pb) { + if (!is_digit(*pa) || !is_digit(*pb)) { + if (*pa != *pb) + return (int)*pa - (int)*pb; + ++pa; ++pb; + } else { + // skip leading zeros + while (*pa == '0') ++pa; + while (*pb == '0') ++pb; + + // skip matching digits + while (is_digit(*pa) && *pa == *pb) + pa++, pb++; + + // Now mismatching, so see which ends the number sooner + int diff = (int)*pa - (int)*pb; + while (is_digit(*pa) && is_digit(*pb)) + pa++, pb++; + + if (is_digit(*pa)) + return 1; // pa still going, so larger + else if (is_digit(*pb)) + return -1; // pb still going, so larger + else if (diff) + return diff; // same length, so earlier diff + } + } + return *pa? 1 : *pb? -1 : 0; +} + + +typedef struct { + htsFile *fp; + bam1_t * b; + bam_hdr_t * hdr; + + uint64_t file_offset; + sds queryname; + int ret; + + aln_spec_t * aln_specs; + uint16_t n_aln_cap; + uint16_t n_aln_sz; + + qidx_record_t * pending_release; +} qidx_record_iter_t; + +qidx_err_t qidx_record_iter_init(qidx_record_iter_t *it, htsFile *fp) { + it->b = bam_init1(); + it->fp = fp; + + // advance past header + it->hdr = sam_hdr_read(fp); + + if(!it->hdr) { + return QIDX_NO_BAM_HDR; + } + + it->file_offset = bgzf_tell(fp->fp.bgzf); + + if((it->ret = sam_read1(it->fp, it->hdr, it->b)) < 0) { + return QIDX_BAM_READ_FAILURE; + } + + it->queryname = sdsnew(bam_get_qname(it->b)); + it->aln_specs = NULL; + it->n_aln_sz = it->n_aln_cap = 0; + + if(bgzf_seek(fp->fp.bgzf, it->file_offset, SEEK_SET) < 0) { + return QIDX_IO_FAIL; + } + + it->pending_release = NULL; + + return QIDX_OK; +} + +static void _qidx_record_iter_free_record(qidx_record_iter_t * it) { + if(it->pending_release) { + free(it->pending_release->alns); + sdsfree(it->pending_release->qname); + it->pending_release = NULL; + } +} + +qidx_err_t qidx_record_iter_next(qidx_record_iter_t * it, qidx_record_t * rec) { + + _qidx_record_iter_free_record(it); + + sds queryname; + int cmp; + int ret; + bool yield = false; + while ((ret = sam_read1(it->fp, it->hdr, it->b)) >= 0) { + queryname = sdsnew(bam_get_qname(it->b)); + + if(!queryname) { + return QIDX_NO_MEM; + } + + if((cmp = strnum_cmp(it->queryname, queryname)) != 0) { + if(cmp > 0) { + printf("Err: the file is not sorted\n"); + return QIDX_NOT_SORTED; + } + + rec->n_alns = it->n_aln_sz; + rec->alns = it->aln_specs; + rec->qname = it->queryname; + + it->pending_release = rec; + + yield = true; + + it->queryname = sdsdup(queryname); + it->aln_specs = NULL; + it->n_aln_cap = it->n_aln_sz = 0; + } + + AM_RESIZE(it->aln_specs, it->n_aln_sz + 1, it->n_aln_cap); + + it->aln_specs[it->n_aln_sz].pos = it->b->core.pos; + it->aln_specs[it->n_aln_sz].tid = it->b->core.tid; + it->aln_specs[it->n_aln_sz].vptr = it->file_offset; + + it->n_aln_sz++; + + // update offset for next record + it->file_offset = bgzf_tell(it->fp->fp.bgzf); + + sdsfree(queryname); + + if(yield) { + break; + } + } + + if(ret < -1) { + it->pending_release = NULL; + return QIDX_BAM_READ_FAILURE; + } else if (ret == -1 && it->queryname != NULL) { + rec->n_alns = it->n_aln_sz; + rec->alns = it->aln_specs; + rec->qname = it->queryname; + + it->pending_release = rec; + + yield = true; + + it->queryname = NULL; + it->aln_specs = NULL; + it->n_aln_cap = it->n_aln_sz = 0; + } + + if(!yield) { + return QIDX_ITER_DONE; + } + + return QIDX_OK; +} + +qidx_err_t qidx_record_iter_destroy(qidx_record_iter_t * it) { + _qidx_record_iter_free_record(it); + + sdsfree(it->queryname); + + bam_hdr_destroy(it->hdr); + bam_destroy1(it->b); + + return QIDX_OK; +} + +#include + +// @abstract Structure containing summary statistics estimated using +// a one-pass algorithm +// @field mu mean +// @field s sample variance +// @field n number of entries +typedef struct { + double mu; + double s; + size_t n; +} roll_est_params_t; + +// @abstract observe a data point +void roll_est_add_evidence(roll_est_params_t * p, double x) { + double delta = x - p->mu; + p->mu += delta / (p->n + 1); + p->s += (x - p->mu) * delta; + p->n++; +} + +// @abstract finalize the estimate +void roll_est_finalize(roll_est_params_t * p) { + p->s /= p->n; +} + +// Calculates the maximum number of items placed into a single bucket +// to not exceed the bucket_size with a probability specified by the +// area to the right of the positive z-score z. E.g. at z=2 there is +// 2.4% chance of the soft limit being exceeded given objects are +// assigned uniformly to each bucket. (The cardinality of each bucket +// is the same.) +// +// In order for the maximum size to (really) not be exceeded, the +// binomial distribution of items in each bucket would need to be +// included. It is recommended to set this soft limit much lower +// than the hard limit to not exceed it. +// +// This is derived from the standard error as measured by the sampling +// distribution. + +// @param soft_limit a soft limit on the number of variable-length items +// stuffed into a single bucket +// @param z the z-score with which this will happen +// @param p the parameters of the normal distribution +size_t estimate_n_buckets(double soft_limit, double z, roll_est_params_t const * p) { + double n = sqrt(z * z * p->s + 4 * p->mu * soft_limit) - z * sqrt(p->s); + n = n / (2 * p->mu); + + int max_bucket_size = floor(n * n); + + return (size_t) ceil((double) p->n / (double) max_bucket_size); +} + +typedef struct { + uint64_t offset; + uint32_t n_bytes; +} qidx_bucket_t; + +typedef struct { + uint32_t n_buckets; + uint32_t max_bucket_size; + qidx_bucket_t * buckets; + char * rb_start; +} qidx_htable_t; + +#define QIDX_MAGIC 0x5d1de6b4 +#define QIDX_VERSION 1 + +#pragma pack(push, 1) + +typedef struct { + uint32_t magic; + uint16_t version; + uint32_t n_buckets; + uint32_t max_bucket_size; +} qidx_header_t; + +#pragma pack(pop) + +typedef struct { + int fd; + void * map; + size_t len; + bool read_only; + qidx_header_t * hdr; + qidx_bucket_t * buckets; + qidx_htable_t * htab; +} qidx_fp_t; + +size_t qidx_file_size(uint32_t n_buckets, uint32_t max_bucket_size) { + size_t sz = 0; + + sz += sizeof(qidx_header_t); + sz += sizeof(qidx_htable_t) * n_buckets; + sz += (uint64_t) n_buckets * (uint64_t) max_bucket_size; + + return sz; +} + +#include +#include + +// @abstract initialize htab, must first populate fp->buckets +qidx_err_t _qidx_init_htab(qidx_fp_t * fp, + uint32_t n_buckets, uint32_t max_bucket_size) { + qidx_htable_t * htab = malloc(sizeof(qidx_htable_t)); + if(!htab) { + return QIDX_NO_MEM; + } + + htab->buckets = calloc(sizeof(qidx_bucket_t), n_buckets); + if(!htab->buckets) { + free(htab); + return QIDX_NO_MEM; + } + + htab->n_buckets = n_buckets; + htab->max_bucket_size = max_bucket_size; + + htab->rb_start = (void *) (fp->buckets + n_buckets); + + fp->htab = htab; + + return QIDX_OK; +} + + +qidx_err_t qidx_open(qidx_fp_t * fp, int fd) { + + fp->fd = fd; + + qidx_header_t hdr; + if(read(fd, &hdr, sizeof(qidx_header_t)) == -1) { + return QIDX_FAILED_TO_OPEN_INDEX_FILE; + } + + if(le32toh(hdr.magic) != QIDX_MAGIC) { + return QIDX_INVALID_MAGIC; + } + + if(le16toh(hdr.version) != QIDX_VERSION) { + return QIDX_INVALID_VERSION; + } + + uint32_t max_bucket_size = le32toh(hdr.max_bucket_size); + uint32_t n_buckets = le32toh(hdr.n_buckets); + + size_t sz = qidx_file_size(n_buckets, max_bucket_size); + + if(lseek(fd, 0, SEEK_SET) == -1) { + return QIDX_IO_FAIL; + } + + fp->read_only = true; + fp->map = mmap(NULL, sz, PROT_READ, MAP_SHARED, fd, 0); + fp->len = sz; + + if(fp->map == MAP_FAILED) { + return QIDX_MAP_FAIL; + } + + fp->hdr = fp->map; + fp->buckets = (qidx_bucket_t *)(fp->hdr + 1); + + qidx_err_t err = _qidx_init_htab(fp, n_buckets, max_bucket_size); + if(err) { return err; } + + for(size_t i = 0; i < n_buckets; i++) { + fp->htab->buckets[i].n_bytes = le32toh(fp->buckets[i].n_bytes); + fp->htab->buckets[i].offset = le64toh(fp->buckets[i].offset); + } + + return QIDX_OK; +} + +qidx_err_t qidx_create(qidx_fp_t * fp, int fd, uint32_t _n_buckets, uint32_t max_bucket_size) { + + uint32_t n_buckets = next_prime_above_lowerbound(_n_buckets); + + size_t sz = qidx_file_size(n_buckets, max_bucket_size); + + fp->fd = fd; + + if(ftruncate(fd, sz) == -1) { + return QIDX_IO_FAIL; + } + + fp->read_only = false; + fp->map = mmap(NULL, sz, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0); + fp->len = sz; + + if(fp->map == MAP_FAILED) { + return QIDX_MAP_FAIL; + } + + fp->hdr = fp->map; + + fp->hdr->magic = htole32(QIDX_MAGIC); + fp->hdr->version = htole16(QIDX_VERSION); + fp->hdr->n_buckets = htole32(n_buckets); + fp->hdr->max_bucket_size = htole32(max_bucket_size); + + fp->buckets = (qidx_bucket_t *) (fp->hdr + 1); + + _qidx_init_htab(fp, n_buckets, max_bucket_size); + + uint64_t off = (char *) fp->htab->rb_start - (char *) fp->map; + for(size_t i = 0; i < n_buckets; i++) { + fp->htab->buckets[i].offset = off; + fp->htab->buckets[i].n_bytes = 0; + off += max_bucket_size; + } + + return QIDX_OK; +} + +qidx_err_t qidx_close(qidx_fp_t * fp) { + + qidx_htable_t * htab = fp->htab; + + if(!fp->read_only) { + for(size_t i = 0; i < htab->n_buckets; i++) { + fp->buckets[i].n_bytes = htole32(htab->buckets[i].n_bytes); + fp->buckets[i].offset = htole64(htab->buckets[i].offset); + } + } + + free(htab->buckets); + free(htab); + + if(munmap(fp->map, fp->len) != -1) { + return QIDX_MAP_FAIL; + } + + return QIDX_OK; +} + +qidx_htable_t * qidx_get_htable(qidx_fp_t * fp) { return fp->htab; } + +static qidx_bucket_t * _qidx_bucket(char const * qname, qidx_htable_t const * tab) { + size_t hash = murmur_hash_str_64s(qname, 0x12345); + + qidx_bucket_t * bucket = &tab->buckets[hash % tab->n_buckets]; + + return bucket; +} + +qidx_err_t qidx_table_add(qidx_htable_t * tab, qidx_record_t const * rec) { + qidx_bucket_t * bucket = _qidx_bucket(rec->qname, tab); + + void * ptr = (char *) tab->rb_start + bucket->offset + bucket->n_bytes; + size_t rem = tab->max_bucket_size - bucket->n_bytes; + + ssize_t wrlen = qidx_record_marital(rec, ptr, rem); + + if(wrlen < 0) { + return QIDX_BUCKET_MAX_SIZE_EXCEEDED; + } + + bucket->n_bytes += wrlen; + + return QIDX_OK; +} + +qidx_err_t qidx_table_get(qidx_htable_t const * tab, + char const * qname, qidx_record_t ** rec) { + qidx_bucket_t * bucket = _qidx_bucket(qname, tab); + + void const * bucket_start = tab->rb_start + bucket->offset; + void const * record_start = + qidx_record_martial_find(bucket_start, bucket->n_bytes, qname); + + if(!record_start) { + *rec = NULL; + } else { + size_t rem = bucket->n_bytes - + ((char const *) record_start - (char const *) bucket_start); + *rec = malloc(sizeof(qidx_record_t)); + + if(!*rec) { return QIDX_NO_MEM; } + + void const * next = qidx_record_unmartial(*rec, record_start, rem); + + if(!next) { + return QIDX_IO_FAIL; + } + } + + return QIDX_OK; +} + +void qidx_die_err(qidx_err_t err) { + char const * errstr = qidx_strerr(err); + if(qidx_errno(err)) { + die_errno("err: %s", errstr); + } else { + die("err: %s", errstr); + } +} + +void qidx_record_print(FILE * file, qidx_record_t * rec) { + fprintf(file, "qname: %s\n", rec->qname); + for(size_t i = 0; i < rec->n_alns; i++) { + fprintf(file, "\tTID: %u\n", rec->alns[i].tid); + fprintf(file, "\tPOS: %u\n", rec->alns[i].pos); + fprintf(file, "\tVPTR: %lu\n", rec->alns[i].vptr); + } +} + +qidx_err_t qidx_create_index(char const * bamfile, char const * indexfile) { + qidx_err_t err; + + htsFile *b_fp = hts_open(bamfile, "r"); + if(b_fp == NULL) { return QIDX_FAILED_TO_OPEN_BAMFILE; } + + // Pass 1: + // - estimate mu, s, n of the distribution of record sizes + // - estimate the number of buckets needed in the hash table + qidx_record_iter_t it; + if((err = qidx_record_iter_init(&it, b_fp))) { + return err; + } + + roll_est_params_t params; + memset(¶ms, 0, sizeof(roll_est_params_t)); + qidx_record_t rec; + while(!(err = qidx_record_iter_next(&it, &rec))) { + double sz = (double) qidx_record_msize(&rec); + roll_est_add_evidence(¶ms, sz); + } + if(err != QIDX_ITER_DONE) return err; + + if ((err = qidx_record_iter_destroy(&it))) { + return err; + } + + roll_est_finalize(¶ms); + + double soft_limit = 8 * 1024; + double z = 5; + uint32_t n_buckets = estimate_n_buckets(soft_limit, z, ¶ms); + uint32_t max_bucket_size = 1 << 24; + + printf("record size (mean): %f\n", params.mu); + printf("record size (variance): %f\n", params.s); + printf("number of records: %zu\n", params.n); + printf("number of buckets: %u\n", n_buckets); + + FILE * qidx = fopen(indexfile, "wb+"); + + if(!qidx) { return QIDX_FAILED_TO_OPEN_INDEX_FILE; } + + int fd = fileno(qidx); + + // PASS 2: + // - add records to index + + // Rewind to start of BAM file + if (-1 == bgzf_seek(b_fp->fp.bgzf, 0, SEEK_SET)) { + return QIDX_IO_FAIL; + } + + qidx_fp_t q_fp; + if((err = qidx_create(&q_fp, fd, n_buckets, max_bucket_size))) { + qidx_die_err(err); + } + + qidx_htable_t * htab = qidx_get_htable(&q_fp); + + if ((err = qidx_record_iter_init(&it, b_fp))) { + return err; + } + + while((err = qidx_record_iter_next(&it, &rec)) == QIDX_OK) { + qidx_table_add(htab, &rec); + } + if(err != QIDX_ITER_DONE) return err; + + if ((err = qidx_record_iter_destroy(&it))) { + return err; + } + + qidx_close(&q_fp); + fclose(qidx); + hts_close(b_fp); + + return QIDX_OK; +} + +qidx_err_t qidx_search_index(char const * indexfile, + char const * bamfile, char const * qname) { + FILE * index = fopen(indexfile, "rb"); + if(!index) { return QIDX_FAILED_TO_OPEN_INDEX_FILE; } + + int fd = fileno(index); + + qidx_fp_t q_fp; + qidx_err_t err = qidx_open(&q_fp, fd); + if(err) return err; + + qidx_htable_t * htab = qidx_get_htable(&q_fp); + + qidx_record_t * rec; + if((err = qidx_table_get(htab, qname, &rec))) { + return err; + } + + if(rec) { + htsFile * fp = hts_open(bamfile, "r"); + htsFile* out_fp = hts_open("-", "w"); + + + if(!fp) { + return QIDX_FAILED_TO_OPEN_BAMFILE; + } + + bam1_t * b = bam_init1(); + bam_hdr_t * hdr = sam_hdr_read(fp); + for(size_t i = 0; i < rec->n_alns; i++) { + aln_spec_t * aln = &rec->alns[i]; + + if(bgzf_seek(fp->fp.bgzf, aln->vptr, SEEK_SET) < 0) { + return QIDX_IO_FAIL; + } + + int ret; + if((ret = sam_read1(fp, hdr, b)) >= 0) { + + int ret = sam_write1(out_fp, hdr, b); + if(ret < 0) { + return QIDX_IO_FAIL; + } + } + } + + sdsfree(rec->qname); + free(rec->alns); + free(rec); + + bam_hdr_destroy(hdr); + bam_destroy1(b); + hts_close(out_fp); + hts_close(fp); + } else { + fprintf(stderr, "Could not find read: %s\n", qname); + } + + return QIDX_OK; +} + +void die_usage(char const * prog) { + err("%s {create,search}", prog); + err(" create [bamfile] [indexfile]"); + die(" search [index] [read]"); +} + +int main(int argc, char ** argv) { + + if(!argc) return 1; + + if(argc < 3) die_usage(argv[0]); + + char const * type = argv[1]; + qidx_err_t err; + + if(strcmp(type, "create") == 0) { + if(argc != 4) die_usage(argv[0]); + char const * bamfile = argv[2]; + char const * indexfile = argv[3]; + err = qidx_create_index(bamfile, indexfile); + if(err) { + qidx_die_err(err); + } + } else if (strcmp(type, "search") == 0) { + if(argc != 5) die_usage(argv[0]); + char const * indexfile = argv[2]; + char const * bamfile = argv[3]; + char const * qname = argv[4]; + if((err = qidx_search_index(indexfile, bamfile, qname))) { + qidx_die_err(err); + } + } else { + die_usage(argv[0]); + } + +} -- cgit v1.2.3