FastBQSR/ext/htslib/cram/mFILE.c

/*
Copyright (c) 2005-2006, 2008-2009, 2013, 2015, 2017-2019 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>

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.
*/

#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>

#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 "../htslib/hts_log.h"
#include "os.h"
#include "mFILE.h"

#ifdef HAVE_MMAP
#include <sys/mman.h>
#endif

/*
 * 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);
        if (!data)
            return NULL;
        bufsize = sb.st_size;
    } else {
        fn = NULL;
    }

    do {
        size_t len;
        if (used + bufsize > allocated) {
            allocated += bufsize;
            char *datan = realloc(data, allocated);
            if (datan) {
                data = datan;
            } else {
                free(data);
                return NULL;
            }
        }
        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;
}


#ifdef HAVE_MMAP
/*
 * mmaps in the file, but only for reading currently.
 *
 * Returns 0 on success
 *        -1 on failure
 */
int mfmmap(mFILE *mf, FILE *fp, const char *fn) {
    struct stat sb;

    if (stat(fn, &sb) != 0)
        return -1;

    mf->size = sb.st_size;
    mf->data = mmap(NULL, mf->size, PROT_READ, MAP_SHARED,
                    fileno(fp), 0);

    if (!mf->data || mf->data == (void *)-1)
        return -1;

    mf->alloced = 0;
    return 0;
}
#endif


/*
 * 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 requiring
 * 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
     * + = for update (read and write)
     * m = mmap (read only)
     */
    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;
    }
#ifdef HAVE_MMAP
    if (strchr(mode_str, 'm'))
        if (!w) mode |= MF_MMAP;
#endif

    if (r) {
        mf = mfcreate(NULL, 0);
        if (NULL == mf) return NULL;
        if (!(mode & MF_TRUNC)) {
#ifdef HAVE_MMAP
            if (mode & MF_MMAP) {
                if (mfmmap(mf, fp, path) == -1) {
                    mf->data = NULL;
                    mode &= ~MF_MMAP;
                }
            }
#endif
            if (!mf->data) {
                mf->data = mfload(fp, path, &mf->size, b);
                if (!mf->data) {
                    free(mf);
                    return NULL;
                }
                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 {
        hts_log_error("Must specify either r, w or a for mode");
        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);

#ifdef HAVE_MMAP
    if ((mf->mode & MF_MMAP) && mf->data) {
        /* Mmaped */
        munmap(mf->data, mf->size);
        mf->data = NULL;
    }
#endif

    if (mf->fp)
        fclose(mf->fp);

    mfdestroy(mf);

    return 0;
}

/*
 * Closes the file pointer contained within the mFILE without destroying
 * the in-memory data.
 *
 * Attempting to do this on an mmaped buffer is an error.
 */
int mfdetach(mFILE *mf) {
    if (!mf)
        return -1;

    mfflush(mf);
    if (mf->mode & MF_MMAP)
        return -1;

    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().
 *
 * Note, we cannot steal the allocated buffer from an mmaped mFILE.
 */

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;

    if (mfdetach(mf) != 0)
        return NULL;

    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;
}

/*
 * 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;
}