[med-svn] [grabix] 08/11: New upstream version 0.1.6
Andreas Tille
tille at debian.org
Thu Dec 7 18:56:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository grabix.
commit 974be90f628b7bb67a65b85a6dcae62ccb938fcd
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 7 19:47:56 2017 +0100
New upstream version 0.1.6
---
Makefile | 2 +
README.md | 44 +
bgzf.c | 710 +
bgzf.h | 211 +
debian/README.Debian | 8 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 32 -
debian/copyright | 36 -
debian/docs | 1 -
debian/grabix.1 | 39 -
debian/grabix.install | 1 -
debian/manpages | 1 -
debian/patches/Hardening.patch | 13 -
debian/patches/series | 3 -
debian/patches/warnings.patch | 29 -
debian/rules | 13 -
debian/source/format | 1 -
debian/watch | 6 -
grabix.cpp | 326 +
grabix.h | 52 +
grabix_main.cpp | 51 +
khash.h | 528 +
simrep.chr1.bed | 72670 +++++++++++++++++++++++++++++++++++++++
test.sh | 78 +
tests/make-test-fastq.py | 9 +
tests/test-fastq.py | 44 +
27 files changed, 74725 insertions(+), 189 deletions(-)
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..65efe0c
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,2 @@
+all:
+ gcc -Wall -O2 -o grabix grabix_main.cpp grabix.cpp bgzf.c -lstdc++ -lz
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..33b8e34
--- /dev/null
+++ b/README.md
@@ -0,0 +1,44 @@
+grabix - a wee tool for random access into BGZF files.
+======================================================
+
+``grabix`` leverages the fantastic BGZF library in ``samtools`` to provide random access into
+text files that have been compressed with ``bgzip``. ``grabix`` creates it's own index (.gbi)
+of the bgzipped file. Once indexed, one can extract arbitrary lines from the file with the ``grab`` command. Or choose random lines with the, well, ``random`` command.
+
+There's a ton of room for improvement, but I needed something quickly in support of a side project.
+
+Here's a brief example using the ``simrep.chr1.bed`` file provided in the repository.
+
+ # 1. compress the file with bgzip
+ bgzip simrep.chr1.bed
+
+ # 2. create a grabix index of the file.
+ # creates simrep.chr1.bed.gbi
+ grabix index simrep.chr1.bed.gz
+
+ # 3. now, extract the 100th line in the file.
+ grabix grab simrep.chr1.bed.gz 100
+ chr1 401285 401444 trf 218
+
+ # 4. extract the 100th through 110th lines in the file.
+ grabix grab simrep.chr1.bed.gz 100 110
+ chr1 401285 401444 trf 218
+ chr1 401573 401748 trf 280
+ chr1 404661 404707 trf 92
+ chr1 406202 406274 trf 76
+ chr1 406227 406286 trf 77
+ chr1 406776 406819 trf 68
+ chr1 409821 409866 trf 51
+ chr1 409865 409900 trf 52
+ chr1 421245 421285 trf 64
+ chr1 422395 422435 trf 80
+ chr1 422560 422588 trf 56
+
+You can also use ``grabix`` to extract random lines from the file
+
+ # extract 10 randome lines from the file using reservoir sampling
+ grabix random simrep.chr1.bed.gz 10
+
+Is a gzipped file bgzipped?
+
+ grabix check simrep.chr1.bed.gz
diff --git a/bgzf.c b/bgzf.c
new file mode 100644
index 0000000..bc1308e
--- /dev/null
+++ b/bgzf.c
@@ -0,0 +1,710 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+ 2011 Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <assert.h>
+#include <pthread.h>
+#include <sys/types.h>
+#include "bgzf.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+typedef knetFile *_bgzf_file_t;
+#define _bgzf_open(fn, mode) knet_open((fn), (mode))
+#define _bgzf_dopen(fd, mode) knet_dopen((fd), (mode))
+#define _bgzf_close(fp) knet_close((knetFile*)(fp))
+#define _bgzf_fileno(fp) (((knetFile*)(fp))->fd)
+#define _bgzf_tell(fp) knet_tell((knetFile*)(fp))
+#define _bgzf_seek(fp, offset, whence) knet_seek((knetFile*)(fp), (offset), (whence))
+#define _bgzf_read(fp, buf, len) knet_read((knetFile*)(fp), (buf), (len))
+#define _bgzf_write(fp, buf, len) knet_write((knetFile*)(fp), (buf), (len))
+#else // ~defined(_USE_KNETFILE)
+#if defined(_WIN32) || defined(_MSC_VER)
+#define ftello(fp) ftell((FILE*)(fp))
+#define fseeko(fp, offset, whence) fseek((FILE*)(fp), (offset), (whence))
+#else // ~defined(_WIN32)
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif // ~defined(_WIN32)
+typedef FILE *_bgzf_file_t;
+#define _bgzf_open(fn, mode) fopen((fn), (mode))
+#define _bgzf_dopen(fd, mode) fdopen(fd, (mode))
+#define _bgzf_close(fp) fclose((FILE*)(fp))
+#define _bgzf_fileno(fp) fileno((FILE*)(fp))
+#define _bgzf_tell(fp) ftello((FILE*)(fp))
+#define _bgzf_seek(fp, offset, whence) fseeko((FILE*)(fp), (offset), (whence))
+#define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
+#define _bgzf_write(fp, buf, len) fwrite((buf), 1, (len), (FILE*)(fp))
+#endif // ~define(_USE_KNETFILE)
+
+#define BLOCK_HEADER_LENGTH 18
+#define BLOCK_FOOTER_LENGTH 8
+
+/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN|
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+*/
+static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";
+
+#ifdef BGZF_CACHE
+typedef struct {
+ int size;
+ uint8_t *block;
+ int64_t end_offset;
+} cache_t;
+#include "khash.h"
+KHASH_MAP_INIT_INT64(cache, cache_t)
+#endif
+
+static inline int ed_is_big()
+{
+ long one= 1;
+ return !(*((char *)(&one)));
+}
+
+static inline void packInt16(uint8_t *buffer, uint16_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+}
+
+static inline int unpackInt16(const uint8_t *buffer)
+{
+ return buffer[0] | buffer[1] << 8;
+}
+
+static inline void packInt32(uint8_t *buffer, uint32_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+ buffer[2] = value >> 16;
+ buffer[3] = value >> 24;
+}
+
+static BGZF *bgzf_read_init()
+{
+ BGZF *fp;
+ fp = (BGZF*)calloc(1, sizeof(BGZF));
+ fp->is_write = 0;
+ fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+#ifdef BGZF_CACHE
+ fp->cache = kh_init(cache);
+#endif
+ return fp;
+}
+
+static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level
+{
+ BGZF *fp;
+ fp = (BGZF*)calloc(1, sizeof(BGZF));
+ fp->is_write = 1;
+ fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+ if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
+ return fp;
+}
+// get the compress level from the mode string
+static int mode2level(const char *__restrict mode)
+{
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i)
+ if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = (int)mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ return compress_level;
+}
+
+BGZF *bgzf_open(const char *path, const char *mode)
+{
+ BGZF *fp = 0;
+ assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_open(path, "r")) == 0) return 0;
+ fp = bgzf_read_init();
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fopen(path, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ fp->is_be = ed_is_big();
+ return fp;
+}
+
+BGZF *bgzf_dopen(int fd, const char *mode)
+{
+ BGZF *fp = 0;
+ assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0;
+ fp = bgzf_read_init();
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fdopen(fd, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ fp->is_be = ed_is_big();
+ return fp;
+}
+
+static int bgzf_compress(void *_dst, int *dlen, void *src, int slen, int level)
+{
+ uint32_t crc;
+ z_stream zs;
+ uint8_t *dst = (uint8_t*)_dst;
+
+ // compress the body
+ zs.zalloc = NULL; zs.zfree = NULL;
+ zs.next_in = (Bytef*)src;
+ zs.avail_in = slen;
+ zs.next_out = dst + BLOCK_HEADER_LENGTH;
+ zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+ if (deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY) != Z_OK) return -1; // -15 to disable zlib header/footer
+ if (deflate(&zs, Z_FINISH) != Z_STREAM_END) return -1;
+ if (deflateEnd(&zs) != Z_OK) return -1;
+ *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
+ // write the header
+ memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block
+ packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes
+ // write the footer
+ crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen);
+ packInt32((uint8_t*)&dst[*dlen - 8], crc);
+ packInt32((uint8_t*)&dst[*dlen - 4], slen);
+ return 0;
+}
+
+// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.
+static int deflate_block(BGZF *fp, int block_length)
+{
+ int comp_size = BGZF_MAX_BLOCK_SIZE;
+ if (bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level) != 0) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ fp->block_offset = 0;
+ return comp_size;
+}
+
+// Inflate the block in fp->compressed_block into fp->uncompressed_block
+static int inflate_block(BGZF* fp, int block_length)
+{
+ z_stream zs;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = (Bytef*)fp->compressed_block + 18;
+ zs.avail_in = block_length - 16;
+ zs.next_out = (Bytef*)fp->uncompressed_block;
+ zs.avail_out = BGZF_MAX_BLOCK_SIZE;
+
+ if (inflateInit2(&zs, -15) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflate(&zs, Z_FINISH) != Z_STREAM_END) {
+ inflateEnd(&zs);
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflateEnd(&zs) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ return zs.total_out;
+}
+
+static int check_header(const uint8_t *header)
+{
+ return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0
+ && unpackInt16((uint8_t*)&header[10]) == 6
+ && header[12] == 'B' && header[13] == 'C'
+ && unpackInt16((uint8_t*)&header[14]) == 2);
+}
+
+#ifdef BGZF_CACHE
+static void free_cache(BGZF *fp)
+{
+ khint_t k;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (fp->is_write) return;
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) free(kh_val(h, k).block);
+ kh_destroy(cache, h);
+}
+
+static int load_block_from_cache(BGZF *fp, int64_t block_address)
+{
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ k = kh_get(cache, h, block_address);
+ if (k == kh_end(h)) return 0;
+ p = &kh_val(h, k);
+ if (fp->block_length != 0) fp->block_offset = 0;
+ fp->block_address = block_address;
+ fp->block_length = p->size;
+ memcpy(fp->uncompressed_block, p->block, BGZF_MAX_BLOCK_SIZE);
+ _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET);
+ return p->size;
+}
+
+static void cache_block(BGZF *fp, int size)
+{
+ int ret;
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return;
+ if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > (uint32_t)fp->cache_size) {
+ /* A better way would be to remove the oldest block in the
+ * cache, but here we remove a random one for simplicity. This
+ * should not have a big impact on performance. */
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) break;
+ if (k < kh_end(h)) {
+ free(kh_val(h, k).block);
+ kh_del(cache, h, k);
+ }
+ }
+ k = kh_put(cache, h, fp->block_address, &ret);
+ if (ret == 0) return; // if this happens, a bug!
+ p = &kh_val(h, k);
+ p->size = fp->block_length;
+ p->end_offset = fp->block_address + size;
+ p->block = (uint8_t*)malloc(BGZF_MAX_BLOCK_SIZE);
+ memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE);
+}
+#else
+static void free_cache(BGZF *fp) {}
+static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
+static void cache_block(BGZF *fp, int size) {}
+#endif
+
+int bgzf_read_block(BGZF *fp)
+{
+ uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
+ int count, size = 0, block_length, remaining;
+ int64_t block_address;
+ block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0;
+ count = _bgzf_read(fp->fp, header, sizeof(header));
+ if (count == 0) { // no data read
+ fp->block_length = 0;
+ return 0;
+ }
+ if (count != sizeof(header) || !check_header(header)) {
+ fp->errcode |= BGZF_ERR_HEADER;
+ return -1;
+ }
+ size = count;
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+ compressed_block = (uint8_t*)fp->compressed_block;
+ memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
+ remaining = block_length - BLOCK_HEADER_LENGTH;
+ count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
+ if (count != remaining) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ size += count;
+ if ((count = inflate_block(fp, block_length)) < 0) return -1;
+ if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek.
+ fp->block_address = block_address;
+ fp->block_length = count;
+ cache_block(fp, size);
+ return 0;
+}
+
+ssize_t bgzf_read(BGZF *fp, void *data, size_t length)
+{
+ ssize_t bytes_read = 0;
+ uint8_t *output = (uint8_t*)data;
+ if (length <= 0) return 0;
+ assert(fp->is_write == 0);
+ while (bytes_read < length) {
+ int copy_length, available = fp->block_length - fp->block_offset;
+ uint8_t *buffer;
+ if (available <= 0) {
+ if (bgzf_read_block(fp) != 0) return -1;
+ available = fp->block_length - fp->block_offset;
+ if (available <= 0) break;
+ }
+ copy_length = length - bytes_read < available? length - bytes_read : available;
+ buffer = (uint8_t*)fp->uncompressed_block;
+ memcpy(output, buffer + fp->block_offset, copy_length);
+ fp->block_offset += copy_length;
+ output += copy_length;
+ bytes_read += copy_length;
+ }
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = fp->block_length = 0;
+ }
+ return bytes_read;
+}
+
+#ifdef BGZF_MT
+
+typedef struct {
+ BGZF *fp;
+ struct mtaux_t *mt;
+ void *buf;
+ int i, errcode, toproc;
+} worker_t;
+
+typedef struct mtaux_t {
+ int n_threads, n_blks, curr, done;
+ volatile int proc_cnt;
+ void **blk;
+ int *len;
+ worker_t *w;
+ pthread_t *tid;
+ pthread_mutex_t lock;
+ pthread_cond_t cv;
+} mtaux_t;
+
+static int worker_aux(worker_t *w)
+{
+ int i, stop = 0;
+ // wait for condition: to process or all done
+ pthread_mutex_lock(&w->mt->lock);
+ while (!w->toproc && !w->mt->done)
+ pthread_cond_wait(&w->mt->cv, &w->mt->lock);
+ if (w->mt->done) stop = 1;
+ w->toproc = 0;
+ pthread_mutex_unlock(&w->mt->lock);
+ if (stop) return 1; // to quit the thread
+ w->errcode = 0;
+ for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) {
+ int clen = BGZF_MAX_BLOCK_SIZE;
+ if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->fp->compress_level) != 0)
+ w->errcode |= BGZF_ERR_ZLIB;
+ memcpy(w->mt->blk[i], w->buf, clen);
+ w->mt->len[i] = clen;
+ }
+ __sync_fetch_and_add(&w->mt->proc_cnt, 1);
+ return 0;
+}
+
+static void *mt_worker(void *data)
+{
+ while (worker_aux((worker_t*)data) == 0);
+ return 0;
+}
+
+int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+{
+ int i;
+ mtaux_t *mt;
+ pthread_attr_t attr;
+ if (!fp->is_write || fp->mt || n_threads <= 1) return -1;
+ mt = (mtaux_t*)calloc(1, sizeof(mtaux_t));
+ mt->n_threads = n_threads;
+ mt->n_blks = n_threads * n_sub_blks;
+ mt->len = (int*)calloc(mt->n_blks, sizeof(int));
+ mt->blk = (void**)calloc(mt->n_blks, sizeof(void*));
+ for (i = 0; i < mt->n_blks; ++i)
+ mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE);
+ mt->tid = (pthread_t*)calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master
+ mt->w = (worker_t*)calloc(mt->n_threads, sizeof(worker_t));
+ for (i = 0; i < mt->n_threads; ++i) {
+ mt->w[i].i = i;
+ mt->w[i].mt = mt;
+ mt->w[i].fp = fp;
+ mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE);
+ }
+ pthread_attr_init(&attr);
+ pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+ pthread_mutex_init(&mt->lock, 0);
+ pthread_cond_init(&mt->cv, 0);
+ for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread
+ pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]);
+ fp->mt = mt;
+ return 0;
+}
+
+static void mt_destroy(mtaux_t *mt)
+{
+ int i;
+ // signal all workers to quit
+ pthread_mutex_lock(&mt->lock);
+ mt->done = 1; mt->proc_cnt = 0;
+ pthread_cond_broadcast(&mt->cv);
+ pthread_mutex_unlock(&mt->lock);
+ for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread
+ // free other data allocated on heap
+ for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]);
+ for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf);
+ free(mt->blk); free(mt->len); free(mt->w); free(mt->tid);
+ pthread_cond_destroy(&mt->cv);
+ pthread_mutex_destroy(&mt->lock);
+ free(mt);
+}
+
+static void mt_queue(BGZF *fp)
+{
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ assert(mt->curr < mt->n_blks); // guaranteed by the caller
+ memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset);
+ mt->len[mt->curr] = fp->block_offset;
+ fp->block_offset = 0;
+ ++mt->curr;
+}
+
+static int mt_flush(BGZF *fp)
+{
+ int i;
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail
+ // signal all the workers to compress
+ pthread_mutex_lock(&mt->lock);
+ for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1;
+ mt->proc_cnt = 0;
+ pthread_cond_broadcast(&mt->cv);
+ pthread_mutex_unlock(&mt->lock);
+ // worker 0 is doing things here
+ worker_aux(&mt->w[0]);
+ // wait for all the threads to complete
+ while (mt->proc_cnt < mt->n_threads);
+ // dump data to disk
+ for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode;
+ for (i = 0; i < mt->curr; ++i)
+ if (fwrite(mt->blk[i], 1, mt->len[i], (FILE*)fp->fp) != (size_t)mt->len[i])
+ fp->errcode |= BGZF_ERR_IO;
+ mt->curr = 0;
+ return 0;
+}
+
+static int mt_lazy_flush(BGZF *fp)
+{
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ if (fp->block_offset) mt_queue(fp);
+ if (mt->curr == mt->n_blks)
+ return mt_flush(fp);
+ return -1;
+}
+
+static ssize_t mt_write(BGZF *fp, const void *data, size_t length)
+{
+ const uint8_t *input = (const uint8_t*)data;
+ ssize_t rest = length;
+ while (rest) {
+ int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest;
+ memcpy((uint8_t*)fp->uncompressed_block + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length; input += copy_length; rest -= copy_length;
+ if (fp->block_offset == BGZF_BLOCK_SIZE) mt_lazy_flush(fp);
+ }
+ return length - rest;
+}
+
+#endif // ~ #ifdef BGZF_MT
+
+int bgzf_flush(BGZF *fp)
+{
+ if (!fp->is_write) return 0;
+#ifdef BGZF_MT
+ if (fp->mt) return mt_flush(fp);
+#endif
+ while (fp->block_offset > 0) {
+ int block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
+ if (fwrite(fp->compressed_block, 1, block_length, (FILE*)fp->fp) != (size_t)block_length) {
+ fp->errcode |= BGZF_ERR_IO; // possibly truncated file
+ return -1;
+ }
+ fp->block_address += block_length;
+ }
+ return 0;
+}
+
+int bgzf_flush_try(BGZF *fp, ssize_t size)
+{
+ if (fp->block_offset + size > BGZF_BLOCK_SIZE) {
+#ifdef BGZF_MT
+ if (fp->mt) return mt_lazy_flush(fp);
+ else return bgzf_flush(fp);
+#else
+ return bgzf_flush(fp);
+#endif
+ }
+ return -1;
+}
+
+ssize_t bgzf_write(BGZF *fp, const void *data, size_t length)
+{
+ const uint8_t *input = (const uint8_t*)data;
+ int block_length = BGZF_BLOCK_SIZE, bytes_written = 0;
+ assert(fp->is_write);
+#ifdef BGZF_MT
+ if (fp->mt) return mt_write(fp, data, length);
+#endif
+ while (bytes_written < length) {
+ uint8_t* buffer = (uint8_t*)fp->uncompressed_block;
+ int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
+ memcpy(buffer + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length;
+ input += copy_length;
+ bytes_written += copy_length;
+ if (fp->block_offset == block_length && bgzf_flush(fp)) break;
+ }
+ return bytes_written;
+}
+
+int bgzf_close(BGZF* fp)
+{
+ int ret, block_length;
+ if (fp == 0) return -1;
+ if (fp->is_write) {
+ if (bgzf_flush(fp) != 0) return -1;
+ fp->compress_level = -1;
+ block_length = deflate_block(fp, 0); // write an empty block
+ fwrite(fp->compressed_block, 1, block_length, (FILE*)fp->fp);
+ if (fflush((FILE*)fp->fp) != 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+#ifdef BGZF_MT
+ if (fp->mt) mt_destroy((mtaux_t*)fp->mt);
+#endif
+ }
+ ret = fp->is_write? fclose((FILE*)fp->fp) : _bgzf_close(fp->fp);
+ if (ret != 0) return -1;
+ free(fp->uncompressed_block);
+ free(fp->compressed_block);
+ free_cache(fp);
+ free(fp);
+ return 0;
+}
+
+void bgzf_set_cache_size(BGZF *fp, int cache_size)
+{
+ if (fp) fp->cache_size = cache_size;
+}
+
+int bgzf_check_EOF(BGZF *fp)
+{
+ uint8_t buf[28];
+ off_t offset;
+ offset = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0;
+ _bgzf_read(fp->fp, buf, 28);
+ _bgzf_seek(fp->fp, offset, SEEK_SET);
+ return (memcmp("\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0", buf, 28) == 0)? 1 : 0;
+}
+
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
+{
+ int block_offset;
+ int64_t block_address;
+
+ if (fp->is_write || where != SEEK_SET) {
+ fp->errcode |= BGZF_ERR_MISUSE;
+ return -1;
+ }
+ block_offset = pos & 0xFFFF;
+ block_address = pos >> 16;
+ if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ fp->block_length = 0; // indicates current block has not been loaded
+ fp->block_address = block_address;
+ fp->block_offset = block_offset;
+ return 0;
+}
+
+int bgzf_is_bgzf(const char *fn)
+{
+ uint8_t buf[16];
+ int n;
+ _bgzf_file_t fp;
+ if ((fp = _bgzf_open(fn, "r")) == 0) return 0;
+ n = _bgzf_read(fp, buf, 16);
+ _bgzf_close(fp);
+ if (n != 16) return 0;
+ return memcmp(g_magic, buf, 16) == 0? 1 : 0;
+}
+
+int bgzf_getc(BGZF *fp)
+{
+ int c;
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
+ if (fp->block_length == 0) return -1; /* end-of-file */
+ }
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ return c;
+}
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+{
+ int l, state = 0;
+ unsigned char *buf = (unsigned char*)fp->uncompressed_block;
+ str->l = 0;
+ do {
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) { state = -2; break; }
+ if (fp->block_length == 0) { state = -1; break; }
+ }
+ for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
+ if (l < fp->block_length) state = 1;
+ l -= fp->block_offset;
+ if (str->l + l + 1 >= str->m) {
+ str->m = str->l + l + 2;
+ kroundup32(str->m);
+ str->s = (char*)realloc(str->s, str->m);
+ }
+ memcpy(str->s + str->l, buf + fp->block_offset, l);
+ str->l += l;
+ fp->block_offset += l + 1;
+ if (fp->block_offset >= fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ } while (state == 0);
+ if (str->l == 0 && state < 0) return state;
+ str->s[str->l] = 0;
+ return str->l;
+}
\ No newline at end of file
diff --git a/bgzf.h b/bgzf.h
new file mode 100644
index 0000000..75d66f7
--- /dev/null
+++ b/bgzf.h
@@ -0,0 +1,211 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+ 2011, 2012 Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+/* The BGZF library was originally written by Bob Handsaker from the Broad
+ * Institute. It was later improved by the SAMtools developers. */
+
+#ifndef __BGZF_H
+#define __BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <sys/types.h>
+
+#define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
+#define BGZF_MAX_BLOCK_SIZE 0x10000
+
+#define BGZF_ERR_ZLIB 1
+#define BGZF_ERR_HEADER 2
+#define BGZF_ERR_IO 4
+#define BGZF_ERR_MISUSE 8
+
+typedef struct {
+ int errcode:16, is_write:2, is_be:2, compress_level:12;
+ int cache_size;
+ int block_length, block_offset;
+ int64_t block_address;
+ void *uncompressed_block, *compressed_block;
+ void *cache; // a pointer to a hash table
+ void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
+#ifdef BGZF_MT
+ void *mt; // only used for multi-threading
+#endif
+} BGZF;
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ /******************
+ * Basic routines *
+ ******************/
+
+ /**
+ * Open an existing file descriptor for reading or writing.
+ *
+ * @param fd file descriptor
+ * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
+ * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
+ * @return BGZF file handler; 0 on error
+ */
+ BGZF* bgzf_dopen(int fd, const char *mode);
+
+ #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
+
+ /**
+ * Open the specified file for reading or writing.
+ */
+ BGZF* bgzf_open(const char* path, const char *mode);
+
+ /**
+ * Close the BGZF and free all associated resources.
+ *
+ * @param fp BGZF file handler
+ * @return 0 on success and -1 on error
+ */
+ int bgzf_close(BGZF *fp);
+
+ /**
+ * Read up to _length_ bytes from the file storing into _data_.
+ *
+ * @param fp BGZF file handler
+ * @param data data array to read into
+ * @param length size of data to read
+ * @return number of bytes actually read; 0 on end-of-file and -1 on error
+ */
+ ssize_t bgzf_read(BGZF *fp, void *data, size_t length);
+
+ /**
+ * Write _length_ bytes from _data_ to the file.
+ *
+ * @param fp BGZF file handler
+ * @param data data array to write
+ * @param length size of data to write
+ * @return number of bytes actually written; -1 on error
+ */
+ ssize_t bgzf_write(BGZF *fp, const void *data, size_t length);
+
+ /**
+ * Write the data in the buffer to the file.
+ */
+ int bgzf_flush(BGZF *fp);
+
+ /**
+ * Return a virtual file pointer to the current location in the file.
+ * No interpetation of the value should be made, other than a subsequent
+ * call to bgzf_seek can be used to position the file at the same point.
+ * Return value is non-negative on success.
+ */
+ #define bgzf_tell(fp) ((((BGZF*)fp)->block_address << 16) | (((BGZF*)fp)->block_offset & 0xFFFF))
+
+ /**
+ * Set the file to read from the location specified by _pos_.
+ *
+ * @param fp BGZF file handler
+ * @param pos virtual file offset returned by bgzf_tell()
+ * @param whence must be SEEK_SET
+ * @return 0 on success and -1 on error
+ */
+ int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
+
+ /**
+ * Check if the BGZF end-of-file (EOF) marker is present
+ *
+ * @param fp BGZF file handler opened for reading
+ * @return 1 if EOF is present; 0 if not or on I/O error
+ */
+ int bgzf_check_EOF(BGZF *fp);
+
+ /**
+ * Check if a file is in the BGZF format
+ *
+ * @param fn file name
+ * @return 1 if _fn_ is BGZF; 0 if not or on I/O error
+ */
+ int bgzf_is_bgzf(const char *fn);
+
+ /*********************
+ * Advanced routines *
+ *********************/
+
+ /**
+ * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+ *
+ * @param fp BGZF file handler
+ * @param size size of cache in bytes; 0 to disable caching (default)
+ */
+ void bgzf_set_cache_size(BGZF *fp, int size);
+
+ /**
+ * Flush the file if the remaining buffer size is smaller than _size_
+ */
+ int bgzf_flush_try(BGZF *fp, ssize_t size);
+
+ /**
+ * Read one byte from a BGZF file. It is faster than bgzf_read()
+ * @param fp BGZF file handler
+ * @return byte read; -1 on end-of-file or error
+ */
+ int bgzf_getc(BGZF *fp);
+
+ /**
+ * Read one line from a BGZF file. It is faster than bgzf_getc()
+ *
+ * @param fp BGZF file handler
+ * @param delim delimitor
+ * @param str string to write to; must be initialized
+ * @return length of the string; 0 on end-of-file; negative on error
+ */
+ int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
+
+ /**
+ * Read the next BGZF block.
+ */
+ int bgzf_read_block(BGZF *fp);
+
+#ifdef BGZF_MT
+ /**
+ * Enable multi-threading (only effective on writing)
+ *
+ * @param fp BGZF file handler; must be opened for writing
+ * @param n_threads #threads used for writing
+ * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended
+ */
+ int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
\ No newline at end of file
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index 05fe611..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,8 +0,0 @@
-grabix for Debian
------------------
-
-The motivation for this package is mostly as a redundancy for
-GEMINI, a Python-based suite for analysing and priorising the
-variations found in next generation sequencing data.
-
- -- Steffen Moeller <moeller at debian.org> Thu, 18 Jul 2013 14:45:55 +0200
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 947d158..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-grabix (0.1.6-1) UNRELEASED; urgency=low
-
- * Initial release.
-
- -- Steffen Moeller <moeller at debian.org> Thu, 18 Jul 2013 14:45:55 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 1840bf8..0000000
--- a/debian/control
+++ /dev/null
@@ -1,32 +0,0 @@
-Source: grabix
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.4
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/grabix/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/grabix/trunk/
-Homepage: https://github.com/arq5x/grabix
-
-Package: grabix
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Description: wee tool for random access into BGZF files
- In biomedical research it is increasing practice to study
- the genetic basis of disease. This now frequently comprises
- the sequencing of human sequences. The output of the machine
- however is redundant, and the real sequence is the best
- sequence to explain the redundancy. The exchange of data
- happens only with compressed files - to huge and redundant
- to perform otherwise. One should avoid uncompression whenever
- possible.
- .
- grabix leverages the fantastic BGZF library of the samtools
- package to provide random access into text files that have
- been compressed with bgzip. grabix creates it's own index
- (.gbi) of the bgzipped file. Once indexed, one can extract
- arbitrary lines from the file with the grab command. Or
- choose random lines with the, well, random command.
-
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index b3d2e66..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,36 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: grabix
-Source: https://github.com/arq5x/grabix
-
-Files: *
-Files: bgzf.c bgzf.h
-Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
- 2011 Attractive Chaos <attractor at live.co.uk>
-
-Files: khash.h
-Copyright: 2008, 2009, 2011 by Attractive Chaos <attractor at live.co.uk>
-License: MIT
-
-Files: debian/*
-Copyright: 2013 Steffen Moeller <moeller at debian.org>
-License: MIT
-
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and associated documentation files (the "Software"),
- to deal in the Software without restriction, including without limitation
- the rights to use, copy, modify, merge, publish, distribute, sublicense,
- and/or sell copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included
- in all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
- CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
- TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
- SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index b43bf86..0000000
--- a/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-README.md
diff --git a/debian/grabix.1 b/debian/grabix.1
deleted file mode 100644
index d5d3781..0000000
--- a/debian/grabix.1
+++ /dev/null
@@ -1,39 +0,0 @@
-.\" Hey, EMACS: -*- nroff -*-
-.\" (C) Copyright 2013 Steffen Moeller <moeller at debian.org>,
-.\"
-.TH GRABIX 1 "July 18, 2013"
-.SH NAME
-grabix \- program to do something
-.SH SYNOPSIS
-.B bgzip
-.RI bedfile
-.br
-.B grabix
-index
-.RI bedfile.gz
-.br
-.B grabix
-grab
-.RI bedfile.gz
-.RI linenumber
-
-.SH DESCRIPTION
-.PP
-In biomedical research it is increasing practice to study
-the genetic basis of disease. This now frequently comprises
-the sequencing of human sequences. The output of the machine
-however is redundant, and the real sequence is the best
-sequence to explain the redundancy. The exchange of data
-happens only with compressed files - to huge and redundant
-to perform otherwise. One should avoid uncompression whenever
-possible.
-.PP
-grabix leverages the fantastic BGZF library of the samtools
-package to provide random access into text files that have
-been compressed with bgzip. grabix creates it's own index
-(.gbi) of the bgzipped file. Once indexed, one can extract
-arbitrary lines from the file with the grab command. Or
-choose random lines with the, well, random command.
-
-.SH SEE ALSO
-.BR https://github.com/arq5x/grabix
diff --git a/debian/grabix.install b/debian/grabix.install
deleted file mode 100644
index 1e29fa1..0000000
--- a/debian/grabix.install
+++ /dev/null
@@ -1 +0,0 @@
-grabix usr/bin
diff --git a/debian/manpages b/debian/manpages
deleted file mode 100644
index 19ee710..0000000
--- a/debian/manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/grabix.1
diff --git a/debian/patches/Hardening.patch b/debian/patches/Hardening.patch
deleted file mode 100644
index 3b6c4fe..0000000
--- a/debian/patches/Hardening.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Index: grabix-0.0~git20130718/Makefile
-===================================================================
---- grabix-0.0~git20130718.orig/Makefile
-+++ grabix-0.0~git20130718/Makefile
-@@ -1,2 +1,7 @@
-+LDFLAGS+= -lstdc++ -lz
-+CFLAGS+=-Wall
- all:
-- gcc -Wall -O2 -o grabix grabix.cpp bgzf.c -lstdc++ -lz
-+ gcc $(CFLAGS) -o grabix grabix.cpp bgzf.c $(LDFLAGS)
-+
-+clean:
-+ rm -f grabix
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 0bca6c9..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,3 +0,0 @@
-Hardening.patch
-warnings.patch
-
diff --git a/debian/patches/warnings.patch b/debian/patches/warnings.patch
deleted file mode 100644
index 5409ce7..0000000
--- a/debian/patches/warnings.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Index: grabix-0.0~git20130718/grabix.cpp
-===================================================================
---- grabix-0.0~git20130718.orig/grabix.cpp
-+++ grabix-0.0~git20130718/grabix.cpp
-@@ -261,7 +261,7 @@
- srand(seed);
-
- // reservoir sample
-- size_t s, N, result_size;
-+ uint64_t N=0, result_size=0;
- vector<string> sample;
- kstring_t *line;
- line = new kstring_t;
-@@ -282,7 +282,7 @@
- }
- else
- {
-- s = (int) ((double)rand()/(double)RAND_MAX * N);
-+ uint64_t s = (uint64_t) ((double)rand()/(double)RAND_MAX * N);
- if (s < K)
- sample[s] = line->s;
- }
-@@ -327,4 +327,4 @@
- }
-
- return EXIT_SUCCESS;
--}
-\ No newline at end of file
-+}
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index a2d43a7..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-# Set default flags with dpkg-buildflags
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/buildflags.mk
-
-%:
- dh $@
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 942921f..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,6 +0,0 @@
-version=4
-
-# Release tag 1.4 is older as 0.1.5 and 0.1.6 -> so this is probably
-# tagged wrongly which is fixed here
-opts="uversionmangle=s/1\.4/0.1.4/" \
- https://github.com/arq5x/grabix/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
diff --git a/grabix.cpp b/grabix.cpp
new file mode 100644
index 0000000..c30ecf2
--- /dev/null
+++ b/grabix.cpp
@@ -0,0 +1,326 @@
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <vector>
+#include <unistd.h>
+using namespace std;
+
+#include "bgzf.h"
+#include "grabix.h"
+
+int usage()
+{
+ cout << "usage: grabix index bgzf_file " << endl;
+ cout << " grabix grab bgzf_file line_start [line_end] " << endl;
+ cout << endl;
+ cout << "examples:" << endl;
+ cout << " # create a grabix index (big.vcf.gz.gbi)" << endl;
+ cout << " grabix index big.vcf.gz" << endl;
+ cout << endl;
+ cout << " # extract the 100th line." << endl;
+ cout << " grabix grab big.vcf.gz 100 [line_end] " << endl;
+ cout << endl;
+ cout << " # extract the 100th through the 200th lines." << endl;
+ cout << " grabix grab big.vcf.gz 100 200 " << endl;
+ cout << endl;
+ cout << " # extract the 100 random lines." << endl;
+ cout << " grabix random big.vcf.gz 100" << endl;
+ cout << endl;
+ cout << " # Is the file bgzipped?" << endl;
+ cout << " grabix check big.vcf.gz" << endl;
+ cout << endl;
+ cout << " # get total number of lines in the file (minus the header)." << endl;
+ cout << " grabix size big.vcf.gz" << endl;
+ cout << "version: " << VERSION << "\n";
+ cout << endl;
+ return EXIT_SUCCESS;
+}
+
+
+bool bgzf_getline_counting(BGZF * stream)
+{
+ int c = -1;
+ while (true)
+ {
+ c = bgzf_getc (stream);
+ if (c == -1)
+ return true;
+ else if (c == 10) // \n
+ return false;
+ }
+}
+
+/*
+Create a gbi index for the file to facilitate
+random access via the BGZF seek utility
+*/
+int create_grabix_index(string bgzf_file)
+{
+ BGZF *bgzf_fp = bgzf_open(bgzf_file.c_str(), "r");
+ if (bgzf_fp == NULL)
+ {
+ cerr << "[grabix] could not open file:" << bgzf_file << endl;
+ exit (1);
+ }
+
+ // create an index for writing
+ string index_file_name = bgzf_file + ".gbi";
+ ofstream index_file(index_file_name.c_str(), ios::out);
+
+ // add the offset for the end of the header to the index
+
+ int status;
+ kstring_t *line = new kstring_t;
+ line->s = '\0';
+ line->l = 0;
+ line->m = 0;
+
+ int64_t prev_offset = 0;
+ int64_t offset = 0;
+ while ((status = bgzf_getline(bgzf_fp, '\n', line)) >= 0)
+ {
+ offset = bgzf_tell (bgzf_fp);
+ if (line->s[0] != '#')
+ break;
+ prev_offset = offset;
+ }
+ index_file << prev_offset << endl;
+
+ // add the offsets for each CHUNK_SIZE
+ // set of records to the index
+ size_t chunk_count = 0;
+ int64_t total_lines = 1;
+ vector<int64_t> chunk_positions;
+ chunk_positions.push_back (prev_offset);
+ bool eof = false;
+ while (true)
+ {
+ // grab the next line and store the offset
+ eof = bgzf_getline_counting(bgzf_fp);
+ offset = bgzf_tell (bgzf_fp);
+ chunk_count++;
+ // stop if we have encountered an empty line
+ if (eof)
+ {
+ if (bgzf_check_EOF(bgzf_fp) == 1) {
+ if (offset > prev_offset) {
+ total_lines++;
+ prev_offset = offset;
+ }
+ break;
+ }
+ }
+ // store the offset of this chunk start
+ else if (chunk_count == CHUNK_SIZE)
+ {
+ chunk_positions.push_back(prev_offset);
+ chunk_count = 0;
+ }
+ total_lines++;
+ prev_offset = offset;
+ }
+ chunk_positions.push_back (prev_offset);
+ bgzf_close(bgzf_fp);
+
+ index_file << total_lines << endl;
+ for (size_t i = 0; i < chunk_positions.size(); ++i)
+ {
+ index_file << chunk_positions[i] << endl;
+ }
+ index_file.close();
+
+ return EXIT_SUCCESS;
+}
+
+/*
+Load an existing gbi index for the file to facilitate
+random access via the BGZF seek utility
+*/
+void load_index(string bgzf_file, index_info &index)
+{
+ string index_file_name = bgzf_file + ".gbi";
+ // open the index file for reading
+ ifstream index_file(index_file_name.c_str(), ios::in);
+
+ if ( !index_file ) {
+ cerr << "[grabix] could not find index file: " << index_file_name << ". Exiting!" << endl;
+ exit (1);
+ }
+ else {
+ string line;
+ getline (index_file, line);
+ index.header_end = atol(line.c_str());
+
+ getline (index_file, line);
+ index.num_lines = atol(line.c_str());
+
+ while (index_file >> line)
+ {
+ index.chunk_offsets.push_back(atol(line.c_str()));
+ }
+ }
+ index_file.close();
+}
+
+
+/*
+Extract lines [FROM, TO] from file.
+*/
+int grab(string bgzf_file, int64_t from_line, int64_t to_line)
+{
+ // load index into vector of offsets
+ index_info index;
+ load_index(bgzf_file, index);
+
+ if (((int) from_line > index.num_lines)
+ ||
+ ((int) to_line > index.num_lines))
+ {
+ cerr << "[grabix] requested lines exceed the number of lines in the file." << endl;
+ exit(1);
+ }
+ else if (from_line < 0)
+ {
+ cerr << "[grabix] indexes must be positive numbers." << endl;
+ exit(1);
+ }
+ else if (from_line > to_line)
+ {
+ cerr << "[grabix] requested end line is less than the requested begin line." << endl;
+ exit(1);
+ }
+ else {
+
+ // load the BGZF file
+ BGZF *bgzf_fp = bgzf_open(bgzf_file.c_str(), "r");
+ if (bgzf_fp == NULL)
+ {
+ cerr << "[grabix] could not open file:" << bgzf_file << endl;
+ exit (1);
+ }
+
+ // dump the header if there is one
+ int status;
+ kstring_t *line = new kstring_t;
+ line->s = '\0';
+ line->l = 0;
+ line->m = 0;
+
+ while ((status = bgzf_getline(bgzf_fp, '\n', line)) != 0)
+ {
+ if (line->s[0] == '#')
+ printf("%s\n", line->s);
+ else break;
+ }
+
+ // easier to work in 0-based space
+ int64_t from_line_0 = from_line - 1;
+ // get the chunk index for the requested line
+ int64_t requested_chunk = from_line_0 / CHUNK_SIZE;
+ // derive the first line in that chunk
+ int64_t chunk_line_start = (requested_chunk * CHUNK_SIZE);
+
+ // jump to the correct offset for the relevant chunk
+ // and fast forward until we find the requested line
+ bgzf_seek (bgzf_fp, index.chunk_offsets[requested_chunk], SEEK_SET);
+ while (chunk_line_start <= from_line_0)
+ {
+ status = bgzf_getline(bgzf_fp, '\n', line);
+ chunk_line_start++;
+ }
+ // now, print each line until we reach the end of the requested block
+ do
+ {
+ printf("%s\n", line->s);
+ status = bgzf_getline(bgzf_fp, '\n', line);
+ chunk_line_start++;
+ } while (chunk_line_start <= to_line);
+ }
+ return EXIT_SUCCESS;
+}
+
+
+/*
+Extract K random lines from file using reservoir sampling
+*/
+int random(string bgzf_file, uint64_t K)
+{
+ // load index into vector of offsets
+ index_info index;
+ load_index(bgzf_file, index);
+
+ if ((int64_t) K > index.num_lines)
+ {
+ cerr << "[grabix] warning: requested more lines than in the file." << endl;
+ exit(1);
+ }
+ else {
+ // load the BGZF file
+ BGZF *bgzf_fp = bgzf_open(bgzf_file.c_str(), "r");
+ if (bgzf_fp == NULL)
+ {
+ cerr << "[grabix] could not open file:" << bgzf_file << endl;
+ exit (1);
+ }
+
+ // seed our random number generator
+ size_t seed = (unsigned)time(0)+(unsigned)getpid();
+ srand(seed);
+
+ // reservoir sample
+ uint64_t s = 0;
+ uint64_t N = 0;
+ uint64_t result_size = 0;
+ vector<string> sample;
+ int status;
+ kstring_t *line = new kstring_t;
+ line->s = '\0';
+ line->l = 0;
+ line->m = 0;
+
+ while ((status = bgzf_getline(bgzf_fp, '\n', line)) != 0)
+ {
+ if (line->s[0] == '#')
+ printf("%s\n", line->s);
+ else break;
+ }
+
+ while ((status = bgzf_getline(bgzf_fp, '\n', line)) != 0)
+ {
+ N++;
+
+ if (status < 0)
+ break;
+
+ if (result_size < K)
+ {
+ sample.push_back(line->s);
+ result_size++;
+ }
+ else
+ {
+ s = (int) ((double)rand()/(double)RAND_MAX * N);
+ if (s < K)
+ sample[s] = line->s;
+ }
+ }
+ bgzf_close(bgzf_fp);
+
+ // report the sample
+ for (size_t i = 0; i < sample.size(); ++i)
+ printf("%s\n", sample[i].c_str());
+
+ }
+ return EXIT_SUCCESS;
+}
+
+/*
+Return the total number of records in the index.
+*/
+int size(string bgzf_file)
+{
+ index_info index;
+ load_index(bgzf_file, index);
+
+ return index.num_lines;
+}
diff --git a/grabix.h b/grabix.h
new file mode 100644
index 0000000..e733f60
--- /dev/null
+++ b/grabix.h
@@ -0,0 +1,52 @@
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <vector>
+using namespace std;
+
+#include "bgzf.h"
+
+
+#define VERSION "0.1.6"
+// we only want to store the offset for every 10000th
+// line. otherwise, were we to store the position of every
+// line in the file, the index could become very large for
+// files with many records.
+#define CHUNK_SIZE 10000
+
+struct index_info {
+ int64_t header_end;
+ vector<int64_t> chunk_offsets;
+ int64_t num_lines;
+};
+
+int usage();
+
+bool bgzf_getline_counting(BGZF * stream);
+
+/*
+Create a gbi index for the file to facilitate
+random access via the BGZF seek utility
+*/
+int create_grabix_index(string bgzf_file);
+
+/*
+Load an existing gbi index for the file to facilitate
+random access via the BGZF seek utility
+*/
+void load_index(string bgzf_file, index_info &index);
+
+/*
+Extract lines [FROM, TO] from file.
+*/
+int grab(string bgzf_file, int64_t from_line, int64_t to_line);
+
+/*
+Extract K random lines from file using reservoir sampling
+*/
+int random(string bgzf_file, uint64_t K);
+
+/*
+Return the total number of records in the index.
+*/
+int size(string bgzf_file);
diff --git a/grabix_main.cpp b/grabix_main.cpp
new file mode 100644
index 0000000..8de1ac5
--- /dev/null
+++ b/grabix_main.cpp
@@ -0,0 +1,51 @@
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <vector>
+using namespace std;
+
+#include "bgzf.h"
+#include "grabix.h"
+
+int main (int argc, char **argv)
+{
+ if (argc == 1) { return usage(); }
+ if (argc >= 3)
+ {
+ // create input file for the purpose of the example
+ string bgzf_file = argv[2];
+
+ string sub_command = argv[1];
+ if (sub_command == "index")
+ {
+ create_grabix_index(bgzf_file);
+ }
+ else if (sub_command == "grab")
+ {
+ int64_t from_line = atol(argv[3]);
+ int64_t to_line = from_line;
+ if (argc == 5)
+ to_line = atol(argv[4]);
+
+ grab(bgzf_file, from_line, to_line);
+ }
+ else if (sub_command == "random")
+ {
+ size_t N = atoi(argv[3]);
+ random(bgzf_file, N);
+ }
+ else if (sub_command == "check")
+ {
+ cout << ((bgzf_is_bgzf(bgzf_file.c_str()) == 1) ? "yes" : "no") << "\n";
+ }
+ else if (sub_command == "size")
+ {
+ cout << size(bgzf_file) << "\n";
+ } else {
+ cout << "unknown command: " << sub_command << endl;
+ cout << "available commands are: index, grab, random, check, size" << endl;
+ }
+ }
+
+ return EXIT_SUCCESS;
+}
diff --git a/khash.h b/khash.h
new file mode 100644
index 0000000..a7e8056
--- /dev/null
+++ b/khash.h
@@ -0,0 +1,528 @@
+/* The MIT License
+
+ Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/*
+ An example:
+
+#include "khash.h"
+KHASH_MAP_INIT_INT(32, char)
+int main() {
+ int ret, is_missing;
+ khiter_t k;
+ khash_t(32) *h = kh_init(32);
+ k = kh_put(32, h, 5, &ret);
+ if (!ret) kh_del(32, h, k);
+ kh_value(h, k) = 10;
+ k = kh_get(32, h, 10);
+ is_missing = (k == kh_end(h));
+ k = kh_get(32, h, 5);
+ kh_del(32, h, k);
+ for (k = kh_begin(h); k != kh_end(h); ++k)
+ if (kh_exist(h, k)) kh_value(h, k) = 1;
+ kh_destroy(32, h);
+ return 0;
+}
+*/
+
+/*
+ 2011-02-14 (0.2.5):
+
+ * Allow to declare global functions.
+
+ 2009-09-26 (0.2.4):
+
+ * Improve portability
+
+ 2008-09-19 (0.2.3):
+
+ * Corrected the example
+ * Improved interfaces
+
+ 2008-09-11 (0.2.2):
+
+ * Improved speed a little in kh_put()
+
+ 2008-09-10 (0.2.1):
+
+ * Added kh_clear()
+ * Fixed a compiling error
+
+ 2008-09-02 (0.2.0):
+
+ * Changed to token concatenation which increases flexibility.
+
+ 2008-08-31 (0.1.2):
+
+ * Fixed a bug in kh_get(), which has not been tested previously.
+
+ 2008-08-31 (0.1.1):
+
+ * Added destructor
+*/
+
+
+#ifndef __AC_KHASH_H
+#define __AC_KHASH_H
+
+/*!
+ @header
+
+ Generic hash table library.
+
+ @copyright Heng Li
+ */
+
+#define AC_VERSION_KHASH_H "0.2.5"
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+/* compipler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifdef _MSC_VER
+#define inline __inline
+#endif
+
+typedef khint32_t khint_t;
+typedef khint_t khiter_t;
+
+#define __ac_HASH_PRIME_SIZE 32
+static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
+{
+ 0ul, 3ul, 11ul, 23ul, 53ul,
+ 97ul, 193ul, 389ul, 769ul, 1543ul,
+ 3079ul, 6151ul, 12289ul, 24593ul, 49157ul,
+ 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul,
+ 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul,
+ 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul,
+ 3221225473ul, 4294967291ul
+};
+
+#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
+#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
+#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
+#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
+#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
+#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
+#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
+
+static const double __ac_HASH_UPPER = 0.77;
+
+#define KHASH_DECLARE(name, khkey_t, khval_t) \
+ typedef struct { \
+ khint_t n_buckets, size, n_occupied, upper_bound; \
+ khint32_t *flags; \
+ khkey_t *keys; \
+ khval_t *vals; \
+ } kh_##name##_t; \
+ extern kh_##name##_t *kh_init_##name(); \
+ extern void kh_destroy_##name(kh_##name##_t *h); \
+ extern void kh_clear_##name(kh_##name##_t *h); \
+ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \
+ extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
+ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
+ extern void kh_del_##name(kh_##name##_t *h, khint_t x);
+
+#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+ typedef struct { \
+ khint_t n_buckets, size, n_occupied, upper_bound; \
+ khint32_t *flags; \
+ khkey_t *keys; \
+ khval_t *vals; \
+ } kh_##name##_t; \
+ SCOPE kh_##name##_t *kh_init_##name() { \
+ return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
+ } \
+ SCOPE void kh_destroy_##name(kh_##name##_t *h) \
+ { \
+ if (h) { \
+ free(h->keys); free(h->flags); \
+ free(h->vals); \
+ free(h); \
+ } \
+ } \
+ SCOPE void kh_clear_##name(kh_##name##_t *h) \
+ { \
+ if (h && h->flags) { \
+ memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ h->size = h->n_occupied = 0; \
+ } \
+ } \
+ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
+ { \
+ if (h->n_buckets) { \
+ khint_t inc, k, i, last; \
+ k = __hash_func(key); i = k % h->n_buckets; \
+ inc = 1 + k % (h->n_buckets - 1); last = i; \
+ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+ else i += inc; \
+ if (i == last) return h->n_buckets; \
+ } \
+ return __ac_iseither(h->flags, i)? h->n_buckets : i; \
+ } else return 0; \
+ } \
+ SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+ { \
+ khint32_t *new_flags = 0; \
+ khint_t j = 1; \
+ { \
+ khint_t t = __ac_HASH_PRIME_SIZE - 1; \
+ while (__ac_prime_list[t] > new_n_buckets) --t; \
+ new_n_buckets = __ac_prime_list[t+1]; \
+ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \
+ else { \
+ new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ if (h->n_buckets < new_n_buckets) { \
+ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+ if (kh_is_map) \
+ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+ } \
+ } \
+ } \
+ if (j) { \
+ for (j = 0; j != h->n_buckets; ++j) { \
+ if (__ac_iseither(h->flags, j) == 0) { \
+ khkey_t key = h->keys[j]; \
+ khval_t val; \
+ if (kh_is_map) val = h->vals[j]; \
+ __ac_set_isdel_true(h->flags, j); \
+ while (1) { \
+ khint_t inc, k, i; \
+ k = __hash_func(key); \
+ i = k % new_n_buckets; \
+ inc = 1 + k % (new_n_buckets - 1); \
+ while (!__ac_isempty(new_flags, i)) { \
+ if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
+ else i += inc; \
+ } \
+ __ac_set_isempty_false(new_flags, i); \
+ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
+ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
+ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
+ __ac_set_isdel_true(h->flags, i); \
+ } else { \
+ h->keys[i] = key; \
+ if (kh_is_map) h->vals[i] = val; \
+ break; \
+ } \
+ } \
+ } \
+ } \
+ if (h->n_buckets > new_n_buckets) { \
+ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
+ if (kh_is_map) \
+ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
+ } \
+ free(h->flags); \
+ h->flags = new_flags; \
+ h->n_buckets = new_n_buckets; \
+ h->n_occupied = h->size; \
+ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
+ } \
+ } \
+ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+ { \
+ khint_t x; \
+ if (h->n_occupied >= h->upper_bound) { \
+ if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
+ else kh_resize_##name(h, h->n_buckets + 1); \
+ } \
+ { \
+ khint_t inc, k, i, site, last; \
+ x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
+ if (__ac_isempty(h->flags, i)) x = i; \
+ else { \
+ inc = 1 + k % (h->n_buckets - 1); last = i; \
+ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+ if (__ac_isdel(h->flags, i)) site = i; \
+ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
+ else i += inc; \
+ if (i == last) { x = site; break; } \
+ } \
+ if (x == h->n_buckets) { \
+ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
+ else x = i; \
+ } \
+ } \
+ } \
+ if (__ac_isempty(h->flags, x)) { \
+ h->keys[x] = key; \
+ __ac_set_isboth_false(h->flags, x); \
+ ++h->size; ++h->n_occupied; \
+ *ret = 1; \
+ } else if (__ac_isdel(h->flags, x)) { \
+ h->keys[x] = key; \
+ __ac_set_isboth_false(h->flags, x); \
+ ++h->size; \
+ *ret = 2; \
+ } else *ret = 0; \
+ return x; \
+ } \
+ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
+ { \
+ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
+ __ac_set_isdel_true(h->flags, x); \
+ --h->size; \
+ } \
+ }
+
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+ KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+/* --- BEGIN OF HASH FUNCTIONS --- */
+
+/*! @function
+ @abstract Integer hash function
+ @param key The integer [khint32_t]
+ @return The hash value [khint_t]
+ */
+#define kh_int_hash_func(key) (khint32_t)(key)
+/*! @function
+ @abstract Integer comparison function
+ */
+#define kh_int_hash_equal(a, b) ((a) == (b))
+/*! @function
+ @abstract 64-bit integer hash function
+ @param key The integer [khint64_t]
+ @return The hash value [khint_t]
+ */
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
+/*! @function
+ @abstract 64-bit integer comparison function
+ */
+#define kh_int64_hash_equal(a, b) ((a) == (b))
+/*! @function
+ @abstract const char* hash function
+ @param s Pointer to a null terminated string
+ @return The hash value
+ */
+static inline khint_t __ac_X31_hash_string(const char *s)
+{
+ khint_t h = *s;
+ if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+ return h;
+}
+/*! @function
+ @abstract Another interface to const char* hash function
+ @param key Pointer to a null terminated string [const char*]
+ @return The hash value [khint_t]
+ */
+#define kh_str_hash_func(key) __ac_X31_hash_string(key)
+/*! @function
+ @abstract Const char* comparison function
+ */
+#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
+
+/* --- END OF HASH FUNCTIONS --- */
+
+/* Other necessary macros... */
+
+/*!
+ @abstract Type of the hash table.
+ @param name Name of the hash table [symbol]
+ */
+#define khash_t(name) kh_##name##_t
+
+/*! @function
+ @abstract Initiate a hash table.
+ @param name Name of the hash table [symbol]
+ @return Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_init(name) kh_init_##name()
+
+/*! @function
+ @abstract Destroy a hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_destroy(name, h) kh_destroy_##name(h)
+
+/*! @function
+ @abstract Reset a hash table without deallocating memory.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_clear(name, h) kh_clear_##name(h)
+
+/*! @function
+ @abstract Resize a hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param s New size [khint_t]
+ */
+#define kh_resize(name, h, s) kh_resize_##name(h, s)
+
+/*! @function
+ @abstract Insert a key to the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Key [type of keys]
+ @param r Extra return code: 0 if the key is present in the hash table;
+ 1 if the bucket is empty (never used); 2 if the element in
+ the bucket has been deleted [int*]
+ @return Iterator to the inserted element [khint_t]
+ */
+#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
+
+/*! @function
+ @abstract Retrieve a key from the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Key [type of keys]
+ @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
+ */
+#define kh_get(name, h, k) kh_get_##name(h, k)
+
+/*! @function
+ @abstract Remove a key from the hash table.
+ @param name Name of the hash table [symbol]
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param k Iterator to the element to be deleted [khint_t]
+ */
+#define kh_del(name, h, k) kh_del_##name(h, k)
+
+
+/*! @function
+ @abstract Test whether a bucket contains data.
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return 1 if containing data; 0 otherwise [int]
+ */
+#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
+
+/*! @function
+ @abstract Get key given an iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return Key [type of keys]
+ */
+#define kh_key(h, x) ((h)->keys[x])
+
+/*! @function
+ @abstract Get value given an iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @param x Iterator to the bucket [khint_t]
+ @return Value [type of values]
+ @discussion For hash sets, calling this results in segfault.
+ */
+#define kh_val(h, x) ((h)->vals[x])
+
+/*! @function
+ @abstract Alias of kh_val()
+ */
+#define kh_value(h, x) ((h)->vals[x])
+
+/*! @function
+ @abstract Get the start iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return The start iterator [khint_t]
+ */
+#define kh_begin(h) (khint_t)(0)
+
+/*! @function
+ @abstract Get the end iterator
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return The end iterator [khint_t]
+ */
+#define kh_end(h) ((h)->n_buckets)
+
+/*! @function
+ @abstract Get the number of elements in the hash table
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return Number of elements in the hash table [khint_t]
+ */
+#define kh_size(h) ((h)->size)
+
+/*! @function
+ @abstract Get the number of buckets in the hash table
+ @param h Pointer to the hash table [khash_t(name)*]
+ @return Number of buckets in the hash table [khint_t]
+ */
+#define kh_n_buckets(h) ((h)->n_buckets)
+
+/* More conenient interfaces */
+
+/*! @function
+ @abstract Instantiate a hash set containing integer keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT(name) \
+ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing integer keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT(name, khval_t) \
+ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing 64-bit integer keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT64(name) \
+ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing 64-bit integer keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT64(name, khval_t) \
+ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+
+typedef const char *kh_cstr_t;
+/*! @function
+ @abstract Instantiate a hash map containing const char* keys
+ @param name Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_STR(name) \
+ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
+
+/*! @function
+ @abstract Instantiate a hash map containing const char* keys
+ @param name Name of the hash table [symbol]
+ @param khval_t Type of values [type]
+ */
+#define KHASH_MAP_INIT_STR(name, khval_t) \
+ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+#endif /* __AC_KHASH_H */
diff --git a/simrep.chr1.bed b/simrep.chr1.bed
new file mode 100644
index 0000000..e4c5fbe
--- /dev/null
+++ b/simrep.chr1.bed
@@ -0,0 +1,72670 @@
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diff --git a/test.sh b/test.sh
new file mode 100644
index 0000000..918f527
--- /dev/null
+++ b/test.sh
@@ -0,0 +1,78 @@
+make
+
+FQ=test.cnt.gz
+rm -f ${FQ}{,.gbi}
+
+lines=50000
+python tests/make-test-fastq.py $lines | bgzip -c > $FQ
+./grabix index $FQ
+python tests/test-fastq.py $FQ
+a=$(grabix grab test.cnt.gz $(($lines * 4)))
+b=$(zless $FQ | tail -1)
+if [[ "$a" != "$b" ]]; then
+ echo FAIL last record
+fi
+rm -f ${FQ}{,.gbi}
+
+for V in \
+ test.PLs.vcf \
+ test.auto_dom.no_parents.2.vcf \
+ test.auto_dom.no_parents.3.vcf \
+ test.auto_dom.no_parents.4.vcf \
+ test.auto_dom.no_parents.5.vcf \
+ test.auto_dom.no_parents.vcf \
+ test.auto_dom.vcf \
+ test.auto_rec.no_parents.2.vcf \
+ test.auto_rec.no_parents.3.vcf \
+ test.auto_rec.no_parents.4.vcf \
+ test.auto_rec.no_parents.5.vcf \
+ test.auto_rec.no_parents.vcf \
+ test.auto_rec.vcf \
+ test.burden.vcf \
+ test.cadd.vcf \
+ test.clinvar.vcf \
+ test.comp_het.2.vcf \
+ test.comp_het.3.vcf \
+ test.comp_het.4.vcf \
+ test.comp_het.5.vcf \
+ test.comp_het.6.vcf \
+ test.comp_het.7.vcf \
+ test.comp_het.vcf \
+ test.cosmic.vcf \
+ test.de_novo.affected.and.unaffected.vcf \
+ test.de_novo.vcf \
+ test.esp.zero.vcf \
+ test.exac.vcf \
+ test.family.vcf \
+ test.fusions.vcf \
+ test.mendel.vcf \
+ test.multiple-alts.decomp.snpeff.vcf \
+ test.passonly.vcf \
+ test.query.vcf \
+ test.region.vep.vcf \
+ test.roh.vcf \
+ test.snpeff.vcf \
+ test.somatic.vcf \
+ test.vcf_id.snpeff.vcf \
+ test1.snpeff.vcf \
+ test2.snpeff.vcf \
+ test3.snpeff.vcf \
+ test4.vep.snpeff.vcf \
+ test5.vep.snpeff.vcf; do
+
+ rm -f ${V}.*
+ wget --quiet https://raw.githubusercontent.com/arq5x/gemini/master/test/$V
+ bgzip -f $V
+ ./grabix index ${V}.gz
+ sleep 1
+ exp=$(zgrep -cv "#" $V.gz)
+ obs=$(./grabix size $V.gz)
+
+ if [[ "$exp" != "$obs" ]]; then
+ echo "FAIL: $V: expected $exp lines found $obs"
+ else
+ echo "OK $V"
+ fi
+ rm -f ${V}.*
+
+done
diff --git a/tests/make-test-fastq.py b/tests/make-test-fastq.py
new file mode 100644
index 0000000..c73b7e7
--- /dev/null
+++ b/tests/make-test-fastq.py
@@ -0,0 +1,9 @@
+import sys
+n = int(sys.argv[1]) + 1
+for i in range(1, n):
+ s = str(i) + "ACTG"
+ print "@read_%i" % i
+ seq = "".join([s] * 20)[:100]
+ print seq
+ print "+"
+ print seq
diff --git a/tests/test-fastq.py b/tests/test-fastq.py
new file mode 100644
index 0000000..390c315
--- /dev/null
+++ b/tests/test-fastq.py
@@ -0,0 +1,44 @@
+import sys
+import subprocess
+import gzip
+
+f = sys.argv[1]
+lines = ["EMPTY"] + [x.strip() for x in gzip.open(f).readlines()]
+
+print "checking indexing at bounds:"
+
+def check(gzname, start, end=None):
+ run = subprocess.check_output
+ exp = lines[start:start+1] if end is None else lines[start:end + 1]
+ obs = run("./grabix grab %s %d" % (gzname, start), shell=True) if end is None \
+ else run("./grabix grab %s %d %d" % (gzname, start, end), shell=True)
+ obs = [x.strip() for x in obs.strip().split("\n")]
+ sys.stdout.write(".")
+ sys.stdout.flush()
+ assert exp == obs, (exp, obs)
+ if start % 4 == 1:
+ assert obs[0][0] == "@"
+ else:
+ assert obs[0][0] != "@"
+
+for i in range(9990, 10010):
+ check(f, i)
+ check(f, i, i + 11)
+ check(f, i, i + 101)
+
+for i in range(19990, 20010):
+ check(f, i)
+ check(f, i, i + 1)
+ check(f, i, i + 4)
+
+for i in range(1, 200):
+ check(f, i)
+ check(f, i, i + 1)
+ check(f, i, i + 4)
+
+n = len(lines)
+
+check(f, n - 1)
+
+print("\nPASS")
+
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/grabix.git
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