ngs_server 0.4 → 0.5

data/ext/tabix/bgzf.h

@@ -0,0 +1,157 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   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.
+*/
+
+#ifndef __BGZF_H
+#define __BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+
+//typedef int8_t bool;
+
+typedef struct {
+    int file_descriptor;
+    char open_mode;  // 'r' or 'w'
+    int16_t owned_file, compress_level;
+#ifdef _USE_KNETFILE
+	union {
+		knetFile *fpr;
+		FILE *fpw;
+	} x;
+#else
+    FILE* file;
+#endif
+    int uncompressed_block_size;
+    int compressed_block_size;
+    void* uncompressed_block;
+    void* compressed_block;
+    int64_t block_address;
+    int block_length;
+    int block_offset;
+	int cache_size;
+    const char* error;
+	void *cache; // a pointer to a hash table
+} BGZF;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Open an existing file descriptor for reading or writing.
+ * Mode must be either "r" or "w".
+ * A subsequent bgzf_close will not close the file descriptor.
+ * Returns null on error.
+ */
+BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
+
+/*
+ * Open the specified file for reading or writing.
+ * Mode must be either "r" or "w".
+ * Returns null on error.
+ */
+BGZF* bgzf_open(const char* path, const char* __restrict mode);
+
+/*
+ * Close the BGZ file and free all associated resources.
+ * Does not close the underlying file descriptor if created with bgzf_fdopen.
+ * Returns zero on success, -1 on error.
+ */
+int bgzf_close(BGZF* fp);
+
+/*
+ * Read up to length bytes from the file storing into data.
+ * Returns the number of bytes actually read.
+ * Returns zero on end of file.
+ * Returns -1 on error.
+ */
+int bgzf_read(BGZF* fp, void* data, int length);
+
+/*
+ * Write length bytes from data to the file.
+ * Returns the number of bytes written.
+ * Returns -1 on error.
+ */
+int bgzf_write(BGZF* fp, const void* data, int length);
+
+/*
+ * 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.
+ * Returns -1 on error.
+ */
+#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
+
+/*
+ * Set the file to read from the location specified by pos, which must
+ * be a value previously returned by bgzf_tell for this file (but not
+ * necessarily one returned by this file handle).
+ * The where argument must be SEEK_SET.
+ * Seeking on a file opened for write is not supported.
+ * Returns zero on success, -1 on error.
+ */
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
+
+/*
+ * Set the cache size. Zero to disable. By default, caching is
+ * disabled. The recommended cache size for frequent random access is
+ * about 8M bytes.
+ */
+void bgzf_set_cache_size(BGZF *fp, int cache_size);
+
+int bgzf_check_EOF(BGZF *fp);
+int bgzf_read_block(BGZF* fp);
+int bgzf_flush(BGZF* fp);
+int bgzf_flush_try(BGZF *fp, int size);
+int bgzf_check_bgzf(const char *fn);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline 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) {
+#ifdef _USE_KNETFILE
+        fp->block_address = knet_tell(fp->x.fpr);
+#else
+        fp->block_address = ftello(fp->file);
+#endif
+        fp->block_offset = 0;
+        fp->block_length = 0;
+    }
+	return c;
+}
+
+#endif

data/ext/tabix/bgzip.c

@@ -0,0 +1,206 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   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 <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <sys/select.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+static const int WINDOW_SIZE = 64 * 1024;
+
+static int bgzip_main_usage()
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Usage:   bgzip [options] [file] ...\n\n");
+	fprintf(stderr, "Options: -c      write on standard output, keep original files unchanged\n");
+	fprintf(stderr, "         -d      decompress\n");
+	fprintf(stderr, "         -f      overwrite files without asking\n");
+	fprintf(stderr, "         -b INT  decompress at virtual file pointer INT\n");
+	fprintf(stderr, "         -s INT  decompress INT bytes in the uncompressed file\n");
+	fprintf(stderr, "         -h      give this help\n");
+	fprintf(stderr, "\n");
+	return 1;
+}
+
+static int write_open(const char *fn, int is_forced)
+{
+	int fd = -1;
+	char c;
+	if (!is_forced) {
+		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
+			fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
+			scanf("%c", &c);
+			if (c != 'Y' && c != 'y') {
+				fprintf(stderr, "[bgzip] not overwritten\n");
+				exit(1);
+			}
+		}
+	}
+	if (fd < 0) {
+		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
+			fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
+			exit(1);
+		}
+	}
+	return fd;
+}
+
+static void fail(BGZF* fp)
+{
+    fprintf(stderr, "Error: %s\n", fp->error);
+    exit(1);
+}
+
+int main(int argc, char **argv)
+{
+	int c, compress, pstdout, is_forced;
+	BGZF *fp;
+	void *buffer;
+	long start, end, size;
+
+	compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+	while((c  = getopt(argc, argv, "cdhfb:s:")) >= 0){
+		switch(c){
+		case 'h': return bgzip_main_usage();
+		case 'd': compress = 0; break;
+		case 'c': pstdout = 1; break;
+		case 'b': start = atol(optarg); break;
+		case 's': size = atol(optarg); break;
+		case 'f': is_forced = 1; break;
+		}
+	}
+	if (size >= 0) end = start + size;
+	if (end >= 0 && end < start) {
+		fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
+		return 1;
+	}
+	if (compress == 1) {
+		struct stat sbuf;
+		int f_src = fileno(stdin);
+		int f_dst = fileno(stdout);
+
+		if ( argc>optind )
+		{
+			if ( stat(argv[optind],&sbuf)<0 ) 
+			{ 
+				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+				return 1; 
+			}
+
+			if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
+				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+				return 1;
+			}
+
+			if (pstdout)
+				f_dst = fileno(stdout);
+			else
+			{
+				char *name = malloc(strlen(argv[optind]) + 5);
+				strcpy(name, argv[optind]);
+				strcat(name, ".gz");
+				f_dst = write_open(name, is_forced);
+				if (f_dst < 0) return 1;
+				free(name);
+			}
+		}
+		else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+			return bgzip_main_usage();
+
+		fp = bgzf_fdopen(f_dst, "w");
+		buffer = malloc(WINDOW_SIZE);
+		while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
+			if (bgzf_write(fp, buffer, c) < 0) fail(fp);
+		// f_dst will be closed here
+		if (bgzf_close(fp) < 0) fail(fp);
+		if (argc > optind && !pstdout) unlink(argv[optind]);
+		free(buffer);
+		close(f_src);
+		return 0;
+	} else {
+		struct stat sbuf;
+		int f_dst;
+
+		if ( argc>optind )
+		{
+			if ( stat(argv[optind],&sbuf)<0 )
+			{
+				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+				return 1;
+			}
+			char *name;
+			int len = strlen(argv[optind]);
+			if ( strcmp(argv[optind]+len-3,".gz") )
+			{
+				fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
+				return 1;
+			}
+			fp = bgzf_open(argv[optind], "r");
+			if (fp == NULL) {
+				fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
+				return 1;
+			}
+
+			if (pstdout) {
+				f_dst = fileno(stdout);
+			}
+			else {
+				name = strdup(argv[optind]);
+				name[strlen(name) - 3] = '\0';
+				f_dst = write_open(name, is_forced);
+				free(name);
+			}
+		}
+		else if (!pstdout && isatty(fileno((FILE *)stdin)) )
+			return bgzip_main_usage();
+		else
+		{
+			f_dst = fileno(stdout);
+			fp = bgzf_fdopen(fileno(stdin), "r");
+			if (fp == NULL) {
+				fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
+				return 1;
+			}
+		}
+		buffer = malloc(WINDOW_SIZE);
+		if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
+		while (1) {
+			if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
+			else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+			if (c == 0) break;
+			if (c < 0) fail(fp);
+			start += c;
+			write(f_dst, buffer, c);
+			if (end >= 0 && start >= end) break;
+		}
+		free(buffer);
+		if (bgzf_close(fp) < 0) fail(fp);
+		if (!pstdout) unlink(argv[optind]);
+		return 0;
+	}
+}

data/ext/tabix/extconf.rb

@@ -0,0 +1 @@
+puts "nothing to do"