restructure library

1 files changed, 40 insertions, 885 deletions

diff --git a/main.c b/main.c
index aa2f3d6..c56a951 100644
--- a/main.c
+++ b/main.c
@@ -1,735 +1,9 @@
 #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;
-}
+#include "util/util.h"
+#include "qidx.h"
 
 void qidx_die_err(qidx_err_t err) {
 	char const * errstr = qidx_strerr(err);
@@ -740,160 +14,10 @@ void qidx_die_err(qidx_err_t err) {
 	}
 }
 
-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]");
+	die("   search [index] [bamfile] [read]");
 }
 
 int main(int argc, char ** argv) {
@@ -904,23 +28,54 @@ int main(int argc, char ** argv) {
 
 	char const * type = argv[1];
 	qidx_err_t err;
+	char const * prog = argv[0];
 
 	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) {
+		int option;
+		uint32_t n_buckets = 0;
+		uint32_t max_bucket_size = 1 << 18;
+
+		while((option = getopt(argc, argv, ":b:s:")) != -1) {
+			switch(option) {
+				case 'b':
+					if(1 != sscanf(optarg, "%u", &n_buckets)) {
+						die("could not parse -b");
+					}
+					break;
+				case 's':
+					if(1 != sscanf(optarg, "%u", &max_bucket_size)) {
+						die("could not parse -s");
+					}
+					break;
+				case ':':
+					die("option needs a value");
+				case '?':
+					die("Unknown option %c", optopt);
+					break;
+			}
+		}
+
+		if(argc - optind != 3) die_usage(prog);
+
+		char const * bamfile = argv[optind + 1];
+		char const * indexfile = argv[optind + 2];
+
+		if((err = qidx_create_index1(bamfile,
+					indexfile, n_buckets, max_bucket_size))) {
 			qidx_die_err(err);
 		}
+
 	} else if (strcmp(type, "search") == 0) {
-		if(argc != 5) die_usage(argv[0]);
+		if(argc != 5) die_usage(prog);
+
 		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]);
 	}