Initial commit

1 files changed, 928 insertions, 0 deletions

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 <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <htslib/sam.h>
+#include <htslib/hts.h>
+#include <htslib/bgzf.h>
+#include <stdbool.h>
+
+#include "util/sds/sds.h"
+#include "util/prime_search.h"
+#include "util/hash.h"
+#include "util/util.h"
+
+#include <endian.h>
+
+// @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 <math.h>
+
+// @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 <sys/mman.h>
+#include <unistd.h>
+
+// @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(&params, 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(&params, sz);
+	}
+	if(err != QIDX_ITER_DONE) return err;
+
+	if ((err = qidx_record_iter_destroy(&it))) {
+		return err;
+	}
+
+	roll_est_finalize(&params);
+
+	double soft_limit = 8 * 1024;
+	double z = 5;
+	uint32_t n_buckets = estimate_n_buckets(soft_limit, z, &params);
+	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]);
+	}
+
+}