diff ezBAMQC/src/htslib/cram/mFILE.c @ 0:dfa3745e5fd8

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/cram/mFILE.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,634 @@
+/*
+Copyright (c) 2005-2006, 2008-2009, 2013 Genome Research Ltd.
+Author: James Bonfield <[e-mail]>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <stdarg.h>
+
+#include "cram/os.h"
+#include "cram/mFILE.h"
+#include "cram/vlen.h"
+
+/*
+ * This file contains memory-based versions of the most commonly used
+ * (by io_lib) stdio functions.
+ *
+ * Actual file IO takes place either on opening or closing an mFILE.
+ *
+ * Coupled to this are a bunch of rather scary macros which can be obtained
+ * by including stdio_hack.h. It is recommended though that you use mFILE.h
+ * instead and replace fopen with mfopen (etc). This is more or less
+ * mandatory if you wish to use both FILE and mFILE structs in a single file.
+ */
+
+static mFILE *m_channel[3];  /* stdin, stdout and stderr fakes */
+
+/*
+ * Reads the entirety of fp into memory. If 'fn' exists it is the filename
+ * associated with fp. This will be used for more optimal reading (via a
+ * stat to identify the size and a single read). Otherwise we use successive
+ * reads until EOF.
+ *
+ * Returns a malloced buffer on success of length *size
+ *         NULL on failure
+ */
+static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) {
+    struct stat sb;
+    char *data = NULL;
+    size_t allocated = 0, used = 0;
+    int bufsize = 8192;
+
+#ifdef _WIN32
+    if (binary)
+	_setmode(_fileno(fp), _O_BINARY);
+    else 
+	_setmode(_fileno(fp), _O_TEXT);
+#endif
+
+    if (fn && -1 != stat(fn, &sb)) {
+	data = malloc(allocated = sb.st_size);
+	bufsize = sb.st_size;
+    } else {
+	fn = NULL;
+    }
+
+    do {
+	size_t len;
+	if (used + bufsize > allocated) {
+	    allocated += bufsize;
+	    data = realloc(data, allocated);
+	}
+	len = fread(data + used, 1, allocated - used, fp);
+	if (len > 0)
+	    used += len;
+    } while (!feof(fp) && (fn == NULL || used < sb.st_size));
+
+    *size = used;
+
+    return data;
+}
+
+/*
+ * Creates and returns m_channel[0].
+ * We initialise this on the first attempted read, which then slurps in
+ * all of stdin until EOF is met.
+ */
+mFILE *mstdin(void) {
+    if (m_channel[0])
+	return m_channel[0];
+
+    m_channel[0] = mfcreate(NULL, 0);
+    if (NULL == m_channel[0]) return NULL;
+    m_channel[0]->fp = stdin;
+    return m_channel[0];
+}
+
+static void init_mstdin(void) {
+    static int done_stdin = 0;
+    if (done_stdin)
+	return;
+
+    m_channel[0]->data = mfload(stdin, NULL, &m_channel[0]->size, 1);
+    m_channel[0]->mode = MF_READ;
+    done_stdin = 1;
+}
+
+/*
+ * Creates and returns m_channel[1]. This is the fake for stdout. It starts as
+ * an empty buffer which is physically written out only when mfflush or
+ * mfclose are called.
+ */
+mFILE *mstdout(void) {
+    if (m_channel[1])
+	return m_channel[1];
+
+    m_channel[1] = mfcreate(NULL, 0);
+    if (NULL == m_channel[1]) return NULL;
+    m_channel[1]->fp = stdout;
+    m_channel[1]->mode = MF_WRITE;
+    return m_channel[1];
+}
+
+/*
+ * Stderr as an mFILE.
+ * The code handles stderr by returning m_channel[2], but also checking
+ * for stderr in fprintf (the common usage of it) to auto-flush.
+ */
+mFILE *mstderr(void) {
+    if (m_channel[2])
+	return m_channel[2];
+
+    m_channel[2] = mfcreate(NULL, 0);
+    if (NULL == m_channel[2]) return NULL;
+    m_channel[2]->fp = stderr;
+    m_channel[2]->mode = MF_WRITE;
+    return m_channel[2];
+}
+
+
+/*
+ * For creating existing mFILE pointers directly from memory buffers.
+ */
+mFILE *mfcreate(char *data, int size) {
+    mFILE *mf = (mFILE *)malloc(sizeof(*mf));
+    if (NULL == mf) return NULL;
+    mf->fp = NULL;
+    mf->data = data;
+    mf->alloced = size;
+    mf->size = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+    mf->mode = MF_READ | MF_WRITE;
+    return mf;
+}
+
+/*
+ * Recreate an existing mFILE to house new data/size.
+ * It also rewinds the file.
+ */
+void mfrecreate(mFILE *mf, char *data, int size) {
+    if (mf->data)
+	free(mf->data);
+    mf->data = data;
+    mf->size = size;
+    mf->alloced = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+}
+
+
+/*
+ * Creates a new mFILE to contain the contents of the FILE pointer.
+ * This mFILE is purely for in-memory operations and has no links to the
+ * original FILE* it came from. It also doesn't close the FILE pointer.
+ * Consider using mfreopen() is you need different behaviour.
+ *
+ * Returns mFILE * on success
+ *         NULL on failure.
+ */ 
+mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp) {
+   mFILE *mf; 
+
+    /* Open using mfreopen() */
+    if (NULL == (mf = mfreopen(path, mode_str, fp)))
+	return NULL;
+    
+    /* Disassociate from the input stream */
+    mf->fp = NULL;
+
+    return mf;
+}
+
+/*
+ * Converts a FILE * to an mFILE *.
+ * Use this for wrapper functions to turn external prototypes requring
+ * FILE * as an argument into internal code using mFILE *.
+ */
+mFILE *mfreopen(const char *path, const char *mode_str, FILE *fp) {
+    mFILE *mf;
+    int r = 0, w = 0, a = 0, b = 0, x = 0, mode = 0;
+
+    /* Parse mode:
+     * r = read file contents (if truncated => don't read)
+     * w = write on close
+     * a = position at end of buffer
+     * x = position at same location as the original fp, don't seek on flush
+     */
+    if (strchr(mode_str, 'r'))
+	r = 1, mode |= MF_READ;
+    if (strchr(mode_str, 'w'))
+	w = 1, mode |= MF_WRITE | MF_TRUNC;
+    if (strchr(mode_str, 'a'))
+	w = a = 1, mode |= MF_WRITE | MF_APPEND;
+    if (strchr(mode_str, 'b'))
+	b = 1, mode |= MF_BINARY;
+    if (strchr(mode_str, 'x'))
+	x = 1;
+    if (strchr(mode_str, '+')) {
+        w = 1, mode |= MF_READ | MF_WRITE;
+	if (a)
+	    r = 1;
+    }
+
+    if (r) {
+	mf = mfcreate(NULL, 0);
+	if (NULL == mf) return NULL;
+	if (!(mode & MF_TRUNC)) {
+	    mf->data = mfload(fp, path, &mf->size, b);
+	    mf->alloced = mf->size;
+	    if (!a)
+		fseek(fp, 0, SEEK_SET);
+	}
+    } else if (w) {
+	/* Write - initialise the data structures */
+	mf = mfcreate(NULL, 0);
+	if (NULL == mf) return NULL;
+    } else {
+        fprintf(stderr, "Must specify either r, w or a for mode\n");
+        return NULL;
+    }
+    mf->fp = fp;
+    mf->mode = mode;
+
+    if (x) {
+	mf->mode |= MF_MODEX;
+    }
+    
+    if (a) {
+	mf->flush_pos = mf->size;
+	fseek(fp, 0, SEEK_END);
+    }
+
+    return mf;
+}
+
+/*
+ * Opens a file. If we have read access (r or a+) then it loads the entire
+ * file into memory. If We have write access then the pathname is stored.
+ * We do not actually write until an mfclose, which then checks this pathname.
+ */
+mFILE *mfopen(const char *path, const char *mode) {
+    FILE *fp;
+
+    if (NULL == (fp = fopen(path, mode)))
+	return NULL;
+    return mfreopen(path, mode, fp);
+}
+
+/*
+ * Closes an mFILE. If the filename is known (implying write access) then this
+ * also writes the data to disk.
+ *
+ * Stdout is handled by calling mfflush which writes to stdout if appropriate.
+ */
+int mfclose(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+
+    if (mf->fp)
+	fclose(mf->fp);
+
+    mfdestroy(mf);
+
+    return 0;
+}
+
+/*
+ * Closes the file pointer contained within the mFILE without destroying
+ * the in-memory data.
+ */
+int mfdetach(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+
+    if (mf->fp) {
+	fclose(mf->fp);
+	mf->fp = NULL;
+    }
+
+    return 0;
+}
+
+/*
+ * Destroys an mFILE structure but does not flush or close it
+ */
+int mfdestroy(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    if (mf->data)
+	free(mf->data);
+    free(mf);
+
+    return 0;
+}
+
+/*
+ * Steals that data out of an mFILE.  The mFILE itself will be closed.
+ * It is up to the caller to free the stolen buffer.  If size_out is
+ * not NULL, mf->size will be stored in it.
+ * This is more-or-less the opposite of mfcreate().
+ */
+
+void *mfsteal(mFILE *mf, size_t *size_out) {
+    void *data;
+
+    if (!mf) return NULL;
+
+    data = mf->data;
+    
+    if (NULL != size_out) *size_out = mf->size;
+
+    mfdetach(mf);
+    mf->data = NULL;
+    mfdestroy(mf);
+
+    return data;
+}
+
+/*
+ * Seek/tell functions. Nothing more than updating and reporting an
+ * in-memory index. NB we can seek on stdin or stdout even provided we
+ * haven't been flushing.
+ */
+int mfseek(mFILE *mf, long offset, int whence) {
+    switch (whence) {
+    case SEEK_SET:
+	mf->offset = offset;
+	break;
+    case SEEK_CUR:
+	mf->offset += offset;
+	break;
+    case SEEK_END:
+	mf->offset = mf->size + offset;
+	break;
+    default:
+	errno = EINVAL;
+	return -1;
+    }
+
+    mf->eof = 0;
+    return 0;
+}
+
+long mftell(mFILE *mf) {
+    return mf->offset;
+}
+
+void mrewind(mFILE *mf) {
+    mf->offset = 0;
+    mf->eof = 0;
+}
+
+/*
+ * mftruncate is not directly a translation of ftruncate as the latter
+ * takes a file descriptor instead of a FILE *. It performs the analogous
+ * role though.
+ *
+ * If offset is -1 then the file is truncated to be the current file
+ * offset.
+ */
+void mftruncate(mFILE *mf, long offset) {
+    mf->size = offset != -1 ? offset : mf->offset;
+    if (mf->offset > mf->size)
+	mf->offset = mf->size;
+}
+
+int mfeof(mFILE *mf) {
+    return mf->eof;
+}
+
+/*
+ * mFILE read/write functions. Basically these turn fread/fwrite syntax
+ * into memcpy statements, with appropriate memory handling for writing.
+ */
+size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    size_t len;
+    char *cptr = (char *)ptr;
+    
+    if (mf == m_channel[0]) init_mstdin();
+
+    if (mf->size <= mf->offset)
+	return 0;
+
+    len = size * nmemb <= mf->size - mf->offset
+	? size * nmemb
+	: mf->size - mf->offset;
+    if (!size)
+	return 0;
+
+    memcpy(cptr, &mf->data[mf->offset], len);
+    mf->offset += len;
+    
+    if (len != size * nmemb) {
+	mf->eof = 1;
+    }
+
+    return len / size;
+}
+
+size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    if (!(mf->mode & MF_WRITE))
+	return 0;
+
+    /* Append mode => forced all writes to end of file */
+    if (mf->mode & MF_APPEND)
+	mf->offset = mf->size;
+
+    /* Make sure we have enough room */
+    while (size * nmemb + mf->offset > mf->alloced) {
+	size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	void * new_data = realloc(mf->data, new_alloced);
+	if (NULL == new_data) return 0;
+	mf->alloced = new_alloced;
+	mf->data    = new_data;
+    }
+
+    /* Record where we need to reflush from */
+    if (mf->offset < mf->flush_pos)
+	mf->flush_pos = mf->offset;
+
+    /* Copy the data over */
+    memcpy(&mf->data[mf->offset], ptr, size * nmemb);
+    mf->offset += size * nmemb;
+    if (mf->size < mf->offset)
+	mf->size = mf->offset;
+
+    return nmemb;
+}
+
+int mfgetc(mFILE *mf) {
+    if (mf == m_channel[0]) init_mstdin();
+    if (mf->offset < mf->size) {
+	return (unsigned char)mf->data[mf->offset++];
+    }
+
+    mf->eof = 1;
+    return -1;
+}
+
+int mungetc(int c, mFILE *mf) {
+    if (mf->offset > 0) {
+	mf->data[--mf->offset] = c;
+	return c;
+    }
+    
+    mf->eof = 1;
+    return -1;
+}
+
+char *mfgets(char *s, int size, mFILE *mf) {
+    int i;
+
+    if (mf == m_channel[0]) init_mstdin();
+    *s = 0;
+    for (i = 0; i < size-1;) {
+	if (mf->offset < mf->size) {
+	    s[i] = mf->data[mf->offset++];
+	    if (s[i++] == '\n')
+		break;
+	} else {
+	    mf->eof = 1;
+	    break;
+	}
+    }
+
+    s[i] = 0;
+    return i ? s : NULL;
+}
+
+/*
+ * Flushes an mFILE. If this is a real open of a file in write mode then
+ * mFILE->fp will be set. We then write out any new data in mFILE since the
+ * last flush. We cannot tell what may have been modified as we don't keep
+ * track of that, so we typically rewrite out the entire file contents between
+ * the last flush_pos and the end of file.
+ *
+ * For stderr/stdout we also reset the offsets so we cannot modify things
+ * we've already output.
+ */
+int mfflush(mFILE *mf) {
+    if (!mf->fp)
+	return 0;
+
+    /* FIXME: only do this when opened in write mode */
+    if (mf == m_channel[1] || mf == m_channel[2]) {
+	if (mf->flush_pos < mf->size) {
+	    size_t bytes = mf->size - mf->flush_pos;
+	    if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes)
+		return -1;
+	    if (0 != fflush(mf->fp))
+		return -1;
+	}
+
+	/* Stdout & stderr are non-seekable streams so throw away the data */
+	mf->offset = mf->size = mf->flush_pos = 0;
+    }
+
+    /* only flush when opened in write mode */
+    if (mf->mode & MF_WRITE) {
+	if (mf->flush_pos < mf->size) {
+	    size_t bytes = mf->size - mf->flush_pos;
+	    if (!(mf->mode & MF_MODEX)) {
+		fseek(mf->fp, mf->flush_pos, SEEK_SET);
+	    }
+	    if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes)
+		return -1;
+	    if (0 != fflush(mf->fp))
+		return -1;
+	}
+	if (ftell(mf->fp) != -1 &&
+	    ftruncate(fileno(mf->fp), ftell(mf->fp)) == -1)
+		return -1;
+	mf->flush_pos = mf->size;
+    }
+
+    return 0;
+}
+
+/*
+ * A wrapper around vsprintf() to write to an mFILE. This also uses vflen() to
+ * estimate how many additional bytes of storage will be required for the
+ * vsprintf to work.
+ */
+int mfprintf(mFILE *mf, char *fmt, ...) {
+    int ret;
+    size_t est_length;
+    va_list args;
+
+    va_start(args, fmt);
+    est_length = vflen(fmt, args);
+    va_end(args);
+    while (est_length + mf->offset > mf->alloced) {
+	size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	void * new_data    = realloc(mf->data, new_alloced);
+	if (NULL == new_data) return -1;
+	mf->alloced = new_alloced;
+	mf->data    = new_data;
+    }
+
+    va_start(args, fmt);
+    ret = vsprintf(&mf->data[mf->offset], fmt, args);
+    va_end(args);
+
+    if (ret > 0) {
+	mf->offset += ret;
+	if (mf->size < mf->offset)
+	    mf->size = mf->offset;
+    }
+
+    if (mf->fp == stderr) {
+	/* Auto-flush for stderr */
+	if (0 != mfflush(mf)) return -1;
+    }
+
+    return ret;
+}
+
+/*
+ * Converts an mFILE from binary to ascii mode by replacing all
+ * cr-nl with nl.
+ *
+ * Primarily used on windows when we've uncompressed a binary file which
+ * happens to be a text file (eg Experiment File). Previously we would have
+ * seeked back to the start and used _setmode(fileno(fp), _O_TEXT).
+ *
+ * Side effect: resets offset and flush_pos back to the start.
+ */
+void mfascii(mFILE *mf) {
+    size_t p1, p2;
+
+    for (p1 = p2 = 1; p1 < mf->size; p1++, p2++) {
+	if (mf->data[p1] == '\n' && mf->data[p1-1] == '\r') {
+	    p2--; /* delete the \r */
+	}
+	mf->data[p2] = mf->data[p1];
+    }
+    mf->size = p2;
+
+    mf->offset = mf->flush_pos = 0;
+}