--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/test_view.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,239 @@
+/*  test/test_view.c -- simple view tool, purely for use in a test harness.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@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 <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cram/cram.h"
+
+#include "htslib/sam.h"
+
+typedef struct hts_opt {
+    enum cram_option opt;
+    union {
+        int i;
+        char *s;
+    } val;
+    struct hts_opt *next;
+} hts_opt;
+
+/*
+ * Parses arg and appends it to the option list.
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int add_option(hts_opt **opts, char *arg) {
+    hts_opt *o, *t;
+    char *cp;
+
+    if (!(cp = strchr(arg, '=')))
+        cp = "1"; // assume boolean
+    else
+        *cp++ = 0;
+
+    if (!(o =  malloc(sizeof(*o))))
+        return -1;
+
+    if (strcmp(arg, "DECODE_MD") == 0)
+        o->opt = CRAM_OPT_DECODE_MD, o->val.i = atoi(cp);
+    else if (strcmp(arg, "VERBOSITY") == 0)
+        o->opt = CRAM_OPT_VERBOSITY, o->val.i = atoi(cp);
+    else if (strcmp(arg, "SEQS_PER_SLICE") == 0)
+        o->opt = CRAM_OPT_SEQS_PER_SLICE, o->val.i = atoi(cp);
+    else if (strcmp(arg, "SLICES_PER_CONTAINER") == 0)
+        o->opt = CRAM_OPT_SLICES_PER_CONTAINER, o->val.i = atoi(cp);
+    else if (strcmp(arg, "EMBED_REF") == 0)
+        o->opt = CRAM_OPT_EMBED_REF, o->val.i = atoi(cp);
+    else if (strcmp(arg, "NO_REF") == 0)
+        o->opt = CRAM_OPT_NO_REF, o->val.i = atoi(cp);
+    else if (strcmp(arg, "IGNORE_MD5") == 0)
+        o->opt = CRAM_OPT_IGNORE_MD5, o->val.i = atoi(cp);
+    else if (strcmp(arg, "USE_BZIP2") == 0)
+        o->opt = CRAM_OPT_USE_BZIP2, o->val.i = atoi(cp);
+    else if (strcmp(arg, "USE_RANS") == 0)
+        o->opt = CRAM_OPT_USE_RANS, o->val.i = atoi(cp);
+    else if (strcmp(arg, "USE_LZMA") == 0)
+        o->opt = CRAM_OPT_USE_LZMA, o->val.i = atoi(cp);
+    else if (strcmp(arg, "REFERENCE") == 0)
+        o->opt = CRAM_OPT_REFERENCE, o->val.s = cp;
+    else if (strcmp(arg, "VERSION") == 0)
+        o->opt = CRAM_OPT_VERSION, o->val.s =cp;
+    else if (strcmp(arg, "MULTI_SEQ_PER_SLICE") == 0)
+        o->opt = CRAM_OPT_MULTI_SEQ_PER_SLICE, o->val.i = atoi(cp);
+    else if (strcmp(arg, "NTHREADS") == 0)
+        o->opt = CRAM_OPT_NTHREADS, o->val.i = atoi(cp);
+    else if (strcmp(arg, "REQUIRED_FIELDS") == 0)
+        o->opt = CRAM_OPT_REQUIRED_FIELDS, o->val.i = strtol(cp, NULL, 0);
+    else {
+        fprintf(stderr, "Unknown option '%s'\n", arg);
+        free(o);
+        return -1;
+    }
+
+    o->next = NULL;
+
+    if (*opts) {
+        t = *opts;
+        while (t->next)
+            t = t->next;
+        t->next = o;
+    } else {
+        *opts = o;
+    }
+
+    return 0;
+}
+
+int main(int argc, char *argv[])
+{
+    samFile *in;
+    char *fn_ref = 0;
+    int flag = 0, c, clevel = -1, ignore_sam_err = 0;
+    char moder[8];
+    bam_hdr_t *h;
+    bam1_t *b;
+    htsFile *out;
+    char modew[8];
+    int r = 0, exit_code = 0;
+    hts_opt *in_opts = NULL, *out_opts = NULL, *last = NULL;
+
+    while ((c = getopt(argc, argv, "IbDCSl:t:i:o:")) >= 0) {
+        switch (c) {
+        case 'S': flag |= 1; break;
+        case 'b': flag |= 2; break;
+        case 'D': flag |= 4; break;
+        case 'C': flag |= 8; break;
+        case 'l': clevel = atoi(optarg); flag |= 2; break;
+        case 't': fn_ref = optarg; break;
+        case 'I': ignore_sam_err = 1; break;
+        case 'i': if (add_option(&in_opts,  optarg)) return 1; break;
+        case 'o': if (add_option(&out_opts, optarg)) return 1; break;
+        }
+    }
+    if (argc == optind) {
+        fprintf(stderr, "Usage: samview [-bSCSI] [-l level] [-o option=value] <in.bam>|<in.sam>|<in.cram> [region]\n");
+        return 1;
+    }
+    strcpy(moder, "r");
+    if (flag&4) strcat(moder, "c");
+    else if ((flag&1) == 0) strcat(moder, "b");
+
+    in = sam_open(argv[optind], moder);
+    if (in == NULL) {
+        fprintf(stderr, "Error opening \"%s\"\n", argv[optind]);
+        return EXIT_FAILURE;
+    }
+    h = sam_hdr_read(in);
+    h->ignore_sam_err = ignore_sam_err;
+    b = bam_init1();
+
+    strcpy(modew, "w");
+    if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
+    if (flag&8) strcat(modew, "c");
+    else if (flag&2) strcat(modew, "b");
+    out = hts_open("-", modew);
+    if (out == NULL) {
+        fprintf(stderr, "Error opening standard output\n");
+        return EXIT_FAILURE;
+    }
+
+    /* CRAM output */
+    if (flag & 8) {
+        // Parse input header and use for CRAM output
+        out->fp.cram->header = sam_hdr_parse_(h->text, h->l_text);
+
+        // Create CRAM references arrays
+        if (fn_ref)
+            cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, fn_ref);
+        else
+            // Attempt to fill out a cram->refs[] array from @SQ headers
+            cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, NULL);
+    }
+
+    // Process any options; currently cram only.
+    for (; in_opts;  in_opts = (last=in_opts)->next, free(last)) {
+        hts_set_opt(in,  in_opts->opt,  in_opts->val);
+        if (in_opts->opt == CRAM_OPT_REFERENCE)
+            hts_set_opt(out,  in_opts->opt,  in_opts->val);
+    }
+    for (; out_opts;  out_opts = (last=out_opts)->next, free(last))
+        hts_set_opt(out, out_opts->opt,  out_opts->val);
+
+    sam_hdr_write(out, h);
+    if (optind + 1 < argc && !(flag&1)) { // BAM input and has a region
+        int i;
+        hts_idx_t *idx;
+        if ((idx = bam_index_load(argv[optind])) == 0) {
+            fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
+            return 1;
+        }
+        for (i = optind + 1; i < argc; ++i) {
+            hts_itr_t *iter;
+            if ((iter = bam_itr_querys(idx, h, argv[i])) == 0) {
+                fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, argv[i]);
+                continue;
+            }
+            while ((r = bam_itr_next(in, iter, b)) >= 0) {
+                if (sam_write1(out, h, b) < 0) {
+                    fprintf(stderr, "Error writing output.\n");
+                    exit_code = 1;
+                    break;
+                }
+            }
+            hts_itr_destroy(iter);
+        }
+        hts_idx_destroy(idx);
+    } else while ((r = sam_read1(in, h, b)) >= 0) {
+        if (sam_write1(out, h, b) < 0) {
+            fprintf(stderr, "Error writing output.\n");
+            exit_code = 1;
+            break;
+        }
+    }
+
+    if (r < -1) {
+        fprintf(stderr, "Error parsing input.\n");
+        exit_code = 1;
+    }
+
+    r = sam_close(out);
+    if (r < 0) {
+        fprintf(stderr, "Error closing output.\n");
+        exit_code = 1;
+    }
+
+    bam_destroy1(b);
+    bam_hdr_destroy(h);
+
+    r = sam_close(in);
+    if (r < 0) {
+        fprintf(stderr, "Error closing input.\n");
+        exit_code = 1;
+    }
+
+    return exit_code;
+}