--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/hfile_irods.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,243 @@
+/*  hfile_irods.c -- iRODS backend for low-level file 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 <stdlib.h>
+#include <string.h>
+#include <errno.h>
+
+#include "hfile_internal.h"
+
+#include <rcConnect.h>
+#include <dataObjOpen.h>
+#include <dataObjRead.h>
+#include <dataObjWrite.h>
+#include <dataObjFsync.h>
+#include <dataObjLseek.h>
+#include <dataObjClose.h>
+
+typedef struct {
+    hFILE base;
+    int descriptor;
+} hFILE_irods;
+
+static int status_errno(int status)
+{
+    switch (status) {
+    case SYS_NO_API_PRIV: return EACCES;
+    case SYS_MALLOC_ERR: return ENOMEM;
+    case SYS_OUT_OF_FILE_DESC: return ENFILE;
+    case SYS_BAD_FILE_DESCRIPTOR: return EBADF;
+    case CAT_NO_ROWS_FOUND: return ENOENT;
+    case CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME: return EEXIST;
+    default: return EIO;
+    }
+}
+
+static void set_errno(int status)
+{
+    int err = abs(status) % 1000;
+    errno = err? err : status_errno(status);
+}
+
+static struct {
+    rcComm_t *conn;
+    rodsEnv env;
+} irods = { NULL };
+
+static void irods_exit()
+{
+    (void) rcDisconnect(irods.conn);
+    irods.conn = NULL;
+}
+
+static int irods_init()
+{
+    rErrMsg_t err;
+    int ret;
+
+    ret = getRodsEnv(&irods.env);
+    if (ret < 0) goto error;
+
+    irods.conn = rcConnect(irods.env.rodsHost, irods.env.rodsPort,
+                           irods.env.rodsUserName, irods.env.rodsZone,
+                           NO_RECONN, &err);
+    if (irods.conn == NULL) { ret = err.status; goto error; }
+
+    if (strcmp(irods.env.rodsUserName, PUBLIC_USER_NAME) != 0) {
+        ret = clientLogin(irods.conn);
+        if (ret != 0) goto error;
+    }
+
+    // In the unlikely event atexit() fails, it's better to succeed here and
+    // carry on and do the I/O; then eventually when the program exits, we'll
+    // merely disconnect from the server uncleanly, as if we had aborted.
+    (void) atexit(irods_exit);
+
+    return 0;
+
+error:
+    if (irods.conn) { (void) rcDisconnect(irods.conn); }
+    irods.conn = NULL;
+    set_errno(ret);
+    return -1;
+}
+
+static ssize_t irods_read(hFILE *fpv, void *buffer, size_t nbytes)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    bytesBuf_t buf;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.len = nbytes;
+
+    buf.buf = buffer;
+    buf.len = nbytes;
+
+    ret = rcDataObjRead(irods.conn, &args, &buf);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static ssize_t irods_write(hFILE *fpv, const void *buffer, size_t nbytes)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    bytesBuf_t buf;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.len = nbytes;
+
+    buf.buf = (void *) buffer; // ...the iRODS API is not const-correct here
+    buf.len = nbytes;
+
+    ret = rcDataObjWrite(irods.conn, &args, &buf);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static off_t irods_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    fileLseekOut_t *out = NULL;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.offset = offset;
+    args.whence = whence;
+
+    ret = rcDataObjLseek(irods.conn, &args, &out);
+
+    if (out) { offset = out->offset; free(out); }
+    else offset = -1;
+    if (ret < 0) { set_errno(ret); return -1; }
+    return offset;
+}
+
+static int irods_flush(hFILE *fpv)
+{
+// FIXME rcDataObjFsync() doesn't seem to function as expected.
+// For now, flush is a no-op: see https://github.com/samtools/htslib/issues/168
+#if 0
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+
+    ret = rcDataObjFsync(irods.conn, &args);
+    if (ret < 0) set_errno(ret);
+    return ret;
+#endif
+    return 0;
+}
+
+static int irods_close(hFILE *fpv)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+
+    ret = rcDataObjClose(irods.conn, &args);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static const struct hFILE_backend irods_backend =
+{
+    irods_read, irods_write, irods_seek, irods_flush, irods_close
+};
+
+hFILE *hopen_irods(const char *filename, const char *mode)
+{
+    hFILE_irods *fp;
+    rodsPath_t path;
+    dataObjInp_t args;
+    int ret;
+
+    // Initialise the iRODS connection if this is the first use.
+    if (irods.conn == NULL) { if (irods_init() < 0) return NULL; }
+
+    if (strncmp(filename, "irods:", 6) == 0) filename += 6;
+    else { errno = EINVAL; return NULL; }
+
+    fp = (hFILE_irods *) hfile_init(sizeof (hFILE_irods), mode, 0);
+    if (fp == NULL) return NULL;
+
+    strncpy(path.inPath, filename, MAX_NAME_LEN-1);
+    path.inPath[MAX_NAME_LEN-1] = '\0';
+
+    ret = parseRodsPath(&path, &irods.env);
+    if (ret < 0) goto error;
+
+    memset(&args, 0, sizeof args);
+    strcpy(args.objPath, path.outPath);
+    args.openFlags = hfile_oflags(mode);
+    if (args.openFlags & O_CREAT) {
+        args.createMode = 0666;
+        addKeyVal(&args.condInput, DEST_RESC_NAME_KW,irods.env.rodsDefResource);
+    }
+
+    ret = rcDataObjOpen(irods.conn, &args);
+    if (ret < 0) goto error;
+    fp->descriptor = ret;
+
+    fp->base.backend = &irods_backend;
+    return &fp->base;
+
+error:
+    hfile_destroy((hFILE *) fp);
+    set_errno(ret);
+    return NULL;
+}