--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/hfile.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,547 @@
+/*  hfile.c -- buffered low-level input/output streams.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18@sanger.ac.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 <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;
+}