--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/faidx.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,475 @@
+/*  faidx.c -- FASTA random access.
+
+    Copyright (C) 2008, 2009, 2013-2015 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    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 <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/faidx.h"
+#include "htslib/hfile.h"
+#include "htslib/khash.h"
+
+typedef struct {
+    int32_t line_len, line_blen;
+    int64_t len;
+    uint64_t offset;
+} faidx1_t;
+KHASH_MAP_INIT_STR(s, faidx1_t)
+
+struct __faidx_t {
+    BGZF *bgzf;
+    int n, m;
+    char **name;
+    khash_t(s) *hash;
+};
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
+{
+    khint_t k;
+    int ret;
+    faidx1_t t;
+    if (idx->n == idx->m) {
+        idx->m = idx->m? idx->m<<1 : 16;
+        idx->name = (char**)realloc(idx->name, sizeof(char*) * idx->m);
+    }
+    idx->name[idx->n] = strdup(name);
+    k = kh_put(s, idx->hash, idx->name[idx->n], &ret);
+    t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset;
+    kh_value(idx->hash, k) = t;
+    ++idx->n;
+}
+
+faidx_t *fai_build_core(BGZF *bgzf)
+{
+    char *name;
+    int c;
+    int l_name, m_name;
+    int line_len, line_blen, state;
+    int l1, l2;
+    faidx_t *idx;
+    uint64_t offset;
+    int64_t len;
+
+    idx = (faidx_t*)calloc(1, sizeof(faidx_t));
+    idx->hash = kh_init(s);
+    name = 0; l_name = m_name = 0;
+    len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
+    while ( (c=bgzf_getc(bgzf))>=0 ) {
+        if (c == '\n') { // an empty line
+            if (state == 1) {
+                offset = bgzf_utell(bgzf);
+                continue;
+            } else if ((state == 0 && len < 0) || state == 2) continue;
+        }
+        if (c == '>') { // fasta header
+            if (len >= 0)
+                fai_insert_index(idx, name, len, line_len, line_blen, offset);
+            l_name = 0;
+            while ( (c=bgzf_getc(bgzf))>=0 && !isspace(c)) {
+                if (m_name < l_name + 2) {
+                    m_name = l_name + 2;
+                    kroundup32(m_name);
+                    name = (char*)realloc(name, m_name);
+                }
+                name[l_name++] = c;
+            }
+            name[l_name] = '\0';
+            if ( c<0 ) {
+                fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+                free(name); fai_destroy(idx);
+                return 0;
+            }
+            if (c != '\n') while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
+            state = 1; len = 0;
+            offset = bgzf_utell(bgzf);
+        } else {
+            if (state == 3) {
+                fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
+                free(name); fai_destroy(idx);
+                return 0;
+            }
+            if (state == 2) state = 3;
+            l1 = l2 = 0;
+            do {
+                ++l1;
+                if (isgraph(c)) ++l2;
+            } while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
+            if (state == 3 && l2) {
+                fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
+                free(name); fai_destroy(idx);
+                return 0;
+            }
+            ++l1; len += l2;
+            if (state == 1) line_len = l1, line_blen = l2, state = 0;
+            else if (state == 0) {
+                if (l1 != line_len || l2 != line_blen) state = 2;
+            }
+        }
+    }
+    if ( name )
+        fai_insert_index(idx, name, len, line_len, line_blen, offset);
+    else
+    {
+        free(idx);
+        return NULL;
+    }
+    free(name);
+    return idx;
+}
+
+void fai_save(const faidx_t *fai, FILE *fp)
+{
+    khint_t k;
+    int i;
+    for (i = 0; i < fai->n; ++i) {
+        faidx1_t x;
+        k = kh_get(s, fai->hash, fai->name[i]);
+        x = kh_value(fai->hash, k);
+#ifdef _WIN32
+        fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
+        fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
+    }
+}
+
+faidx_t *fai_read(FILE *fp)
+{
+    faidx_t *fai;
+    char *buf, *p;
+    int len, line_len, line_blen;
+#ifdef _WIN32
+    long offset;
+#else
+    long long offset;
+#endif
+    fai = (faidx_t*)calloc(1, sizeof(faidx_t));
+    fai->hash = kh_init(s);
+    buf = (char*)calloc(0x10000, 1);
+    while (!feof(fp) && fgets(buf, 0x10000, fp)) {
+        for (p = buf; *p && isgraph(*p); ++p);
+        *p = 0; ++p;
+#ifdef _WIN32
+        sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
+        sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
+        fai_insert_index(fai, buf, len, line_len, line_blen, offset);
+    }
+    free(buf);
+    return fai;
+}
+
+void fai_destroy(faidx_t *fai)
+{
+    int i;
+    for (i = 0; i < fai->n; ++i) free(fai->name[i]);
+    free(fai->name);
+    kh_destroy(s, fai->hash);
+    if (fai->bgzf) bgzf_close(fai->bgzf);
+    free(fai);
+}
+
+int fai_build(const char *fn)
+{
+    char *str;
+    BGZF *bgzf;
+    FILE *fp;
+    faidx_t *fai;
+    str = (char*)calloc(strlen(fn) + 5, 1);
+    sprintf(str, "%s.fai", fn);
+    bgzf = bgzf_open(fn, "r");
+    if ( !bgzf ) {
+        fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
+        free(str);
+        return -1;
+    }
+    if ( bgzf->is_compressed ) bgzf_index_build_init(bgzf);
+    fai = fai_build_core(bgzf);
+    if ( !fai )
+    {
+        if ( bgzf->is_compressed && bgzf->is_gzip ) fprintf(stderr,"Cannot index files compressed with gzip, please use bgzip\n");
+        free(str);
+        return -1;
+    }
+    if ( bgzf->is_compressed ) bgzf_index_dump(bgzf, fn, ".gzi");
+    bgzf_close(bgzf);
+    fp = fopen(str, "wb");
+    if ( !fp ) {
+        fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
+        fai_destroy(fai); free(str);
+        return -1;
+    }
+    fai_save(fai, fp);
+    fclose(fp);
+    free(str);
+    fai_destroy(fai);
+    return 0;
+}
+
+static FILE *download_and_open(const char *fn)
+{
+    const int buf_size = 1 * 1024 * 1024;
+    uint8_t *buf;
+    FILE *fp;
+    hFILE *fp_remote;
+    const char *url = fn;
+    const char *p;
+    int l = strlen(fn);
+    for (p = fn + l - 1; p >= fn; --p)
+        if (*p == '/') break;
+    fn = p + 1;
+
+    // First try to open a local copy
+    fp = fopen(fn, "r");
+    if (fp)
+        return fp;
+
+    // If failed, download from remote and open
+    fp_remote = hopen(url, "rb");
+    if (fp_remote == 0) {
+        fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+        return NULL;
+    }
+    if ((fp = fopen(fn, "wb")) == 0) {
+        fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+        hclose_abruptly(fp_remote);
+        return NULL;
+    }
+    buf = (uint8_t*)calloc(buf_size, 1);
+    while ((l = hread(fp_remote, buf, buf_size)) > 0)
+        fwrite(buf, 1, l, fp);
+    free(buf);
+    fclose(fp);
+    if (hclose(fp_remote) != 0)
+        fprintf(stderr, "[download_from_remote] fail to close remote file %s\n", url);
+
+    return fopen(fn, "r");
+}
+
+faidx_t *fai_load(const char *fn)
+{
+    char *str;
+    FILE *fp;
+    faidx_t *fai;
+    str = (char*)calloc(strlen(fn) + 5, 1);
+    sprintf(str, "%s.fai", fn);
+
+    if (hisremote(str))
+    {
+        fp = download_and_open(str);
+        if ( !fp )
+        {
+            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+            free(str);
+            return 0;
+        }
+    }
+    else
+        fp = fopen(str, "rb");
+
+    if (fp == 0) {
+        fprintf(stderr, "[fai_load] build FASTA index.\n");
+        fai_build(fn);
+        fp = fopen(str, "rb");
+        if (fp == 0) {
+            fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
+            free(str);
+            return 0;
+        }
+    }
+
+    fai = fai_read(fp);
+    fclose(fp);
+
+    fai->bgzf = bgzf_open(fn, "rb");
+    free(str);
+    if (fai->bgzf == 0) {
+        fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+        return 0;
+    }
+    if ( fai->bgzf->is_compressed==1 )
+    {
+        if ( bgzf_index_load(fai->bgzf, fn, ".gzi") < 0 )
+        {
+            fprintf(stderr, "[fai_load] failed to load .gzi index: %s[.gzi]\n", fn);
+            fai_destroy(fai);
+            return NULL;
+        }
+    }
+    return fai;
+}
+
+char *fai_fetch(const faidx_t *fai, const char *str, int *len)
+{
+    char *s;
+    int c, i, l, k, name_end;
+    khiter_t iter;
+    faidx1_t val;
+    khash_t(s) *h;
+    int beg, end;
+
+    beg = end = -1;
+    h = fai->hash;
+    name_end = l = strlen(str);
+    s = (char*)malloc(l+1);
+    // remove space
+    for (i = k = 0; i < l; ++i)
+        if (!isspace(str[i])) s[k++] = str[i];
+    s[k] = 0; l = k;
+    // determine the sequence name
+    for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+    if (i >= 0) name_end = i;
+    if (name_end < l) { // check if this is really the end
+        int n_hyphen = 0;
+        for (i = name_end + 1; i < l; ++i) {
+            if (s[i] == '-') ++n_hyphen;
+            else if (!isdigit(s[i]) && s[i] != ',') break;
+        }
+        if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+        s[name_end] = 0;
+        iter = kh_get(s, h, s);
+        if (iter == kh_end(h)) { // cannot find the sequence name
+            iter = kh_get(s, h, str); // try str as the name
+            if (iter == kh_end(h)) {
+                *len = 0;
+            free(s); return 0;
+            } else s[name_end] = ':', name_end = l;
+        }
+    } else iter = kh_get(s, h, str);
+    if(iter == kh_end(h)) {
+        fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+        free(s);
+        *len = -2;
+        return 0;
+    };
+    val = kh_value(h, iter);
+    // parse the interval
+    if (name_end < l) {
+        for (i = k = name_end + 1; i < l; ++i)
+            if (s[i] != ',') s[k++] = s[i];
+        s[k] = 0;
+        beg = atoi(s + name_end + 1);
+        for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+        end = i < k? atoi(s + i + 1) : val.len;
+        if (beg > 0) --beg;
+    } else beg = 0, end = val.len;
+    if (beg >= val.len) beg = val.len;
+    if (end >= val.len) end = val.len;
+    if (beg > end) beg = end;
+    free(s);
+
+    // now retrieve the sequence
+    int ret = bgzf_useek(fai->bgzf, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
+    if ( ret<0 )
+    {
+        *len = -1;
+        fprintf(stderr, "[fai_fetch] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
+        return NULL;
+    }
+    l = 0;
+    s = (char*)malloc(end - beg + 2);
+    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < end - beg )
+        if (isgraph(c)) s[l++] = c;
+    s[l] = '\0';
+    *len = l;
+    return s;
+}
+
+int faidx_fetch_nseq(const faidx_t *fai)
+{
+    return fai->n;
+}
+
+int faidx_nseq(const faidx_t *fai)
+{
+    return fai->n;
+}
+
+const char *faidx_iseq(const faidx_t *fai, int i)
+{
+    return fai->name[i];
+}
+
+int faidx_seq_len(const faidx_t *fai, const char *seq)
+{
+    khint_t k = kh_get(s, fai->hash, seq);
+    if ( k == kh_end(fai->hash) ) return -1;
+    return kh_val(fai->hash, k).len;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+    int l, c;
+    khiter_t iter;
+    faidx1_t val;
+    char *seq=NULL;
+
+    // Adjust position
+    iter = kh_get(s, fai->hash, c_name);
+    if (iter == kh_end(fai->hash))
+    {
+        *len = -2;
+        fprintf(stderr, "[fai_fetch_seq] The sequence \"%s\" not found\n", c_name);
+        return NULL;
+    }
+    val = kh_value(fai->hash, iter);
+    if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+    if(p_beg_i < 0) p_beg_i = 0;
+    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+    if(p_end_i < 0) p_end_i = 0;
+    else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+    // Now retrieve the sequence
+    int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+    if ( ret<0 )
+    {
+        *len = -1;
+        fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
+        return NULL;
+    }
+    l = 0;
+    seq = (char*)malloc(p_end_i - p_beg_i + 2);
+    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
+        if (isgraph(c)) seq[l++] = c;
+    seq[l] = '\0';
+    *len = l;
+    return seq;
+}
+
+int faidx_has_seq(const faidx_t *fai, const char *seq)
+{
+    khiter_t iter = kh_get(s, fai->hash, seq);
+    if (iter == kh_end(fai->hash)) return 0;
+    return 1;
+}
+