annotate ezBAMQC/src/htslib/hfile.c @ 17:161866cee2a2

wrapper rename

/*  hfile.c -- buffered low-level input/output streams.

    Copyright (C) 2013-2015 Genome Research Ltd.

    Author: John Marshall <[e-mail]>

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 <errno.h>

#include "htslib/hfile.h"
#include "hfile_internal.h"

/* hFILE fields are used as follows:

   char *buffer;     // Pointer to the start of the I/O buffer
   char *begin;      // First not-yet-read character / unused position
   char *end;        // First unfilled/unfillable position
   char *limit;      // Pointer to the first position past the buffer

   const hFILE_backend *backend;  // Methods to refill/flush I/O buffer

   off_t offset;     // Offset within the stream of buffer position 0
   int at_eof:1;     // For reading, whether EOF has been seen
   int has_errno;    // Error number from the last failure on this stream

For reading, begin is the first unread character in the buffer and end is the
first unfilled position:

   -----------ABCDEFGHIJKLMNO---------------
   ^buffer    ^begin         ^end           ^limit

For writing, begin is the first unused position and end is unused so remains
equal to buffer:

   ABCDEFGHIJKLMNOPQRSTUVWXYZ---------------
   ^buffer                   ^begin         ^limit
   ^end

Thus if begin > end then there is a non-empty write buffer, if begin < end
then there is a non-empty read buffer, and if begin == end then both buffers
are empty.  In all cases, the stream's file position indicator corresponds
to the position pointed to by begin.  */

hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity)
{
    hFILE *fp = (hFILE *) malloc(struct_size);
    if (fp == NULL) goto error;

    if (capacity == 0) capacity = 32768;
    // FIXME For now, clamp input buffer sizes so mpileup doesn't eat memory
    if (strchr(mode, 'r') && capacity > 32768) capacity = 32768;

    fp->buffer = (char *) malloc(capacity);
    if (fp->buffer == NULL) goto error;

    fp->begin = fp->end = fp->buffer;
    fp->limit = &fp->buffer[capacity];

    fp->offset = 0;
    fp->at_eof = 0;
    fp->has_errno = 0;
    return fp;

error:
    hfile_destroy(fp);
    return NULL;
}

void hfile_destroy(hFILE *fp)
{
    int save = errno;
    if (fp) free(fp->buffer);
    free(fp);
    errno = save;
}

static inline int writebuffer_is_nonempty(hFILE *fp)
{
    return fp->begin > fp->end;
}

/* Refills the read buffer from the backend (once, so may only partially
   fill the buffer), returning the number of additional characters read
   (which might be 0), or negative when an error occurred.  */
static ssize_t refill_buffer(hFILE *fp)
{
    ssize_t n;

    // Move any unread characters to the start of the buffer
    if (fp->begin > fp->buffer) {
        fp->offset += fp->begin - fp->buffer;
        memmove(fp->buffer, fp->begin, fp->end - fp->begin);
        fp->end = &fp->buffer[fp->end - fp->begin];
        fp->begin = fp->buffer;
    }

    // Read into the available buffer space at fp->[end,limit)
    if (fp->at_eof || fp->end == fp->limit) n = 0;
    else {
        n = fp->backend->read(fp, fp->end, fp->limit - fp->end);
        if (n < 0) { fp->has_errno = errno; return n; }
        else if (n == 0) fp->at_eof = 1;
    }

    fp->end += n;
    return n;
}

/* Called only from hgetc(), when our buffer is empty.  */
int hgetc2(hFILE *fp)
{
    return (refill_buffer(fp) > 0)? (unsigned char) *(fp->begin++) : EOF;
}

ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes)
{
    size_t n = fp->end - fp->begin;
    while (n < nbytes) {
        ssize_t ret = refill_buffer(fp);
        if (ret < 0) return ret;
        else if (ret == 0) break;
        else n += ret;
    }

    if (n > nbytes) n = nbytes;
    memcpy(buffer, fp->begin, n);
    return n;
}

/* Called only from hread(); when called, our buffer is empty and nread bytes
   have already been placed in the destination buffer.  */
ssize_t hread2(hFILE *fp, void *destv, size_t nbytes, size_t nread)
{
    const size_t capacity = fp->limit - fp->buffer;
    char *dest = (char *) destv;
    dest += nread, nbytes -= nread;

    // Read large requests directly into the destination buffer
    while (nbytes * 2 >= capacity && !fp->at_eof) {
        ssize_t n = fp->backend->read(fp, dest, nbytes);
        if (n < 0) { fp->has_errno = errno; return n; }
        else if (n == 0) fp->at_eof = 1;
        fp->offset += n;
        dest += n, nbytes -= n;
        nread += n;
    }

    while (nbytes > 0 && !fp->at_eof) {
        size_t n;
        ssize_t ret = refill_buffer(fp);
        if (ret < 0) return ret;

        n = fp->end - fp->begin;
        if (n > nbytes) n = nbytes;
        memcpy(dest, fp->begin, n);
        fp->begin += n;
        dest += n, nbytes -= n;
        nread += n;
    }

    return nread;
}

/* Flushes the write buffer, fp->[buffer,begin), out through the backend
   returning 0 on success or negative if an error occurred.  */
static ssize_t flush_buffer(hFILE *fp)
{
    const char *buffer = fp->buffer;
    while (buffer < fp->begin) {
        ssize_t n = fp->backend->write(fp, buffer, fp->begin - buffer);
        if (n < 0) { fp->has_errno = errno; return n; }
        buffer += n;
        fp->offset += n;
    }

    fp->begin = fp->buffer;  // Leave the buffer empty
    return 0;
}

int hflush(hFILE *fp)
{
    if (flush_buffer(fp) < 0) return EOF;
    if (fp->backend->flush(fp) < 0) { fp->has_errno = errno; return EOF; }
    return 0;
}

/* Called only from hputc(), when our buffer is already full.  */
int hputc2(int c, hFILE *fp)
{
    if (flush_buffer(fp) < 0) return EOF;
    *(fp->begin++) = c;
    return c;
}

/* Called only from hwrite() and hputs2(); when called, our buffer is full and
   ncopied bytes from the source have already been copied to our buffer.  */
ssize_t hwrite2(hFILE *fp, const void *srcv, size_t totalbytes, size_t ncopied)
{
    const char *src = (const char *) srcv;
    ssize_t ret;
    const size_t capacity = fp->limit - fp->buffer;
    size_t remaining = totalbytes - ncopied;
    src += ncopied;

    ret = flush_buffer(fp);
    if (ret < 0) return ret;

    // Write large blocks out directly from the source buffer
    while (remaining * 2 >= capacity) {
        ssize_t n = fp->backend->write(fp, src, remaining);
        if (n < 0) { fp->has_errno = errno; return n; }
        fp->offset += n;
        src += n, remaining -= n;
    }

    // Just buffer any remaining characters
    memcpy(fp->begin, src, remaining);
    fp->begin += remaining;

    return totalbytes;
}

/* Called only from hputs(), when our buffer is already full.  */
int hputs2(const char *text, size_t totalbytes, size_t ncopied, hFILE *fp)
{
    return (hwrite2(fp, text, totalbytes, ncopied) >= 0)? 0 : EOF;
}

off_t hseek(hFILE *fp, off_t offset, int whence)
{
    off_t pos;

    if (writebuffer_is_nonempty(fp)) {
        int ret = flush_buffer(fp);
        if (ret < 0) return ret;
    }
    else {
        // Convert relative offsets from being relative to the hFILE's stream
        // position (at begin) to being relative to the backend's physical
        // stream position (at end, due to the buffering read-ahead).
        if (whence == SEEK_CUR) offset -= fp->end - fp->begin;
    }

    pos = fp->backend->seek(fp, offset, whence);
    if (pos < 0) { fp->has_errno = errno; return pos; }

    // Seeking succeeded, so discard any non-empty read buffer
    fp->begin = fp->end = fp->buffer;
    fp->at_eof = 0;

    fp->offset = pos;
    return pos;
}

int hclose(hFILE *fp)
{
    int err = fp->has_errno;

    if (writebuffer_is_nonempty(fp) && hflush(fp) < 0) err = fp->has_errno;
    if (fp->backend->close(fp) < 0) err = errno;
    hfile_destroy(fp);

    if (err) {
        errno = err;
        return EOF;
    }
    else return 0;
}

void hclose_abruptly(hFILE *fp)
{
    int save = errno;
    if (fp->backend->close(fp) < 0) { /* Ignore subsequent errors */ }
    hfile_destroy(fp);
    errno = save;
}


/***************************
 * File descriptor backend *
 ***************************/

#include <sys/socket.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>

#ifdef _WIN32
#define HAVE_CLOSESOCKET
#endif

/* For Unix, it doesn't matter whether a file descriptor is a socket.
   However Windows insists on send()/recv() and its own closesocket()
   being used when fd happens to be a socket.  */

typedef struct {
    hFILE base;
    int fd;
    int is_socket:1;
} hFILE_fd;

static ssize_t fd_read(hFILE *fpv, void *buffer, size_t nbytes)
{
    hFILE_fd *fp = (hFILE_fd *) fpv;
    ssize_t n;
    do {
        n = fp->is_socket? recv(fp->fd, buffer, nbytes, 0)
                         : read(fp->fd, buffer, nbytes);
    } while (n < 0 && errno == EINTR);
    return n;
}

static ssize_t fd_write(hFILE *fpv, const void *buffer, size_t nbytes)
{
    hFILE_fd *fp = (hFILE_fd *) fpv;
    ssize_t n;
    do {
        n = fp->is_socket?  send(fp->fd, buffer, nbytes, 0)
                         : write(fp->fd, buffer, nbytes);
    } while (n < 0 && errno == EINTR);
    return n;
}

static off_t fd_seek(hFILE *fpv, off_t offset, int whence)
{
    hFILE_fd *fp = (hFILE_fd *) fpv;
    return lseek(fp->fd, offset, whence);
}

static int fd_flush(hFILE *fpv)
{
    hFILE_fd *fp = (hFILE_fd *) fpv;
    int ret;
    do {
#ifdef HAVE_FDATASYNC
        ret = fdatasync(fp->fd);
#else
        ret = fsync(fp->fd);
#endif
        // Ignore invalid-for-fsync(2) errors due to being, e.g., a pipe,
        // and operation-not-supported errors (Mac OS X)
        if (ret < 0 && (errno == EINVAL || errno == ENOTSUP)) ret = 0;
    } while (ret < 0 && errno == EINTR);
    return ret;
}

static int fd_close(hFILE *fpv)
{
    hFILE_fd *fp = (hFILE_fd *) fpv;
    int ret;
    do {
#ifdef HAVE_CLOSESOCKET
        ret = fp->is_socket? closesocket(fp->fd) : close(fp->fd);
#else
        ret = close(fp->fd);
#endif
    } while (ret < 0 && errno == EINTR);
    return ret;
}

static const struct hFILE_backend fd_backend =
{
    fd_read, fd_write, fd_seek, fd_flush, fd_close
};

static size_t blksize(int fd)
{
    struct stat sbuf;
    if (fstat(fd, &sbuf) != 0) return 0;
    return sbuf.st_blksize;
}

static hFILE *hopen_fd(const char *filename, const char *mode)
{
    hFILE_fd *fp = NULL;
    int fd = open(filename, hfile_oflags(mode), 0666);
    if (fd < 0) goto error;

    fp = (hFILE_fd *) hfile_init(sizeof (hFILE_fd), mode, blksize(fd));
    if (fp == NULL) goto error;

    fp->fd = fd;
    fp->is_socket = 0;
    fp->base.backend = &fd_backend;
    return &fp->base;

error:
    if (fd >= 0) { int save = errno; (void) close(fd); errno = save; }
    hfile_destroy((hFILE *) fp);
    return NULL;
}

hFILE *hdopen(int fd, const char *mode)
{
    hFILE_fd *fp = (hFILE_fd*) hfile_init(sizeof (hFILE_fd), mode, blksize(fd));
    if (fp == NULL) return NULL;

    fp->fd = fd;
    fp->is_socket = (strchr(mode, 's') != NULL);
    fp->base.backend = &fd_backend;
    return &fp->base;
}

static hFILE *hopen_fd_stdinout(const char *mode)
{
    int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO;
    // TODO Set binary mode (for Windows)
    return hdopen(fd, mode);
}

int hfile_oflags(const char *mode)
{
    int rdwr = 0, flags = 0;
    const char *s;
    for (s = mode; *s; s++)
        switch (*s) {
        case 'r': rdwr = O_RDONLY;  break;
        case 'w': rdwr = O_WRONLY; flags |= O_CREAT | O_TRUNC;  break;
        case 'a': rdwr = O_WRONLY; flags |= O_CREAT | O_APPEND;  break;
        case '+': rdwr = O_RDWR;  break;
        default:  break;
        }

#ifdef O_BINARY
    flags |= O_BINARY;
#endif

    return rdwr | flags;
}


/*********************
 * In-memory backend *
 *********************/

typedef struct {
    hFILE base;
    const char *buffer;
    size_t length, pos;
} hFILE_mem;

static ssize_t mem_read(hFILE *fpv, void *buffer, size_t nbytes)
{
    hFILE_mem *fp = (hFILE_mem *) fpv;
    size_t avail = fp->length - fp->pos;
    if (nbytes > avail) nbytes = avail;
    memcpy(buffer, fp->buffer + fp->pos, nbytes);
    fp->pos += nbytes;
    return nbytes;
}

static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
{
    hFILE_mem *fp = (hFILE_mem *) fpv;
    size_t absoffset = (offset >= 0)? offset : -offset;
    size_t origin;

    switch (whence) {
    case SEEK_SET: origin = 0; break;
    case SEEK_CUR: origin = fp->pos; break;
    case SEEK_END: origin = fp->length; break;
    default: errno = EINVAL; return -1;
    }

    if ((offset  < 0 && absoffset > origin) ||
        (offset >= 0 && absoffset > fp->length - origin)) {
        errno = EINVAL;
        return -1;
    }

    fp->pos = origin + offset;
    return fp->pos;
}

static int mem_close(hFILE *fpv)
{
    return 0;
}

static const struct hFILE_backend mem_backend =
{
    mem_read, NULL, mem_seek, NULL, mem_close
};

static hFILE *hopen_mem(const char *data, const char *mode)
{
    // TODO Implement write modes, which will require memory allocation
    if (strchr(mode, 'r') == NULL) { errno = EINVAL; return NULL; }

    hFILE_mem *fp = (hFILE_mem *) hfile_init(sizeof (hFILE_mem), mode, 0);
    if (fp == NULL) return NULL;

    fp->buffer = data;
    fp->length = strlen(data);
    fp->pos = 0;
    fp->base.backend = &mem_backend;
    return &fp->base;
}


/******************************
 * hopen() backend dispatcher *
 ******************************/

hFILE *hopen(const char *fname, const char *mode)
{
    if (strncmp(fname, "http://", 7) == 0 ||
        strncmp(fname, "ftp://", 6) == 0) return hopen_net(fname, mode);
#ifdef HAVE_IRODS
    else if (strncmp(fname, "irods:", 6) == 0) return hopen_irods(fname, mode);
#endif
    else if (strncmp(fname, "data:", 5) == 0) return hopen_mem(fname + 5, mode);
    else if (strcmp(fname, "-") == 0) return hopen_fd_stdinout(mode);
    else return hopen_fd(fname, mode);
}

int hisremote(const char *fname)
{
    // FIXME Make a new backend entry to return this
    if (strncmp(fname, "http://", 7) == 0 ||
        strncmp(fname, "https://", 8) == 0 ||
        strncmp(fname, "ftp://", 6) == 0) return 1;
#ifdef HAVE_IRODS
    else if (strncmp(fname, "irods:", 6) == 0) return 1;
#endif
    else return 0;
}