--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/bam_import.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,480 @@
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <assert.h>
+#ifdef _WIN32
+#include <fcntl.h>
+#endif
+#include "kstring.h"
+#include "bam.h"
+#include "sam_header.h"
+#include "kseq.h"
+#include "khash.h"
+
+KSTREAM_INIT(gzFile, gzread, 8192)
+KHASH_MAP_INIT_STR(ref, uint64_t)
+
+void bam_init_header_hash(bam_header_t *header);
+void bam_destroy_header_hash(bam_header_t *header);
+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
+
+unsigned char bam_nt16_table[256] = {
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
+	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
+};
+
+unsigned short bam_char2flag_table[256] = {
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+	BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
+char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
+
+struct __tamFile_t {
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t *str;
+	uint64_t n_lines;
+	int is_first;
+};
+
+char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
+{
+	char **list = 0, *s;
+	int n = 0, dret, m = 0;
+	gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+	kstream_t *ks;
+	kstring_t *str;
+	str = (kstring_t*)calloc(1, sizeof(kstring_t));
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, '\n', str, &dret) > 0) {
+		if (n == m) {
+			m = m? m << 1 : 16;
+			list = (char**)realloc(list, m * sizeof(char*));
+		}
+		if (str->s[str->l-1] == '\r')
+			str->s[--str->l] = '\0';
+		s = list[n++] = (char*)calloc(str->l + 1, 1);
+		strcpy(s, str->s);
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	free(str->s); free(str);
+	*_n = n;
+	return list;
+}
+
+static bam_header_t *hash2header(const kh_ref_t *hash)
+{
+	bam_header_t *header;
+	khiter_t k;
+	header = bam_header_init();
+	header->n_targets = kh_size(hash);
+	header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
+	header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
+	for (k = kh_begin(hash); k != kh_end(hash); ++k) {
+		if (kh_exist(hash, k)) {
+			int i = (int)kh_value(hash, k);
+			header->target_name[i] = (char*)kh_key(hash, k);
+			header->target_len[i] = kh_value(hash, k)>>32;
+		}
+	}
+	bam_init_header_hash(header);
+	return header;
+}
+bam_header_t *sam_header_read2(const char *fn)
+{
+	bam_header_t *header;
+	int c, dret, ret, error = 0;
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t *str;
+	kh_ref_t *hash;
+	khiter_t k;
+	if (fn == 0) return 0;
+	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+	if (fp == 0) return 0;
+	hash = kh_init(ref);
+	ks = ks_init(fp);
+	str = (kstring_t*)calloc(1, sizeof(kstring_t));
+	while (ks_getuntil(ks, 0, str, &dret) > 0) {
+		char *s = strdup(str->s);
+		int len, i;
+		i = kh_size(hash);
+		ks_getuntil(ks, 0, str, &dret);
+		len = atoi(str->s);
+		k = kh_put(ref, hash, s, &ret);
+		if (ret == 0) {
+			fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
+			error = 1;
+		}
+		kh_value(hash, k) = (uint64_t)len<<32 | i;
+		if (dret != '\n')
+			while ((c = ks_getc(ks)) != '\n' && c != -1);
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	free(str->s); free(str);
+	fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
+	if (error) return 0;
+	header = hash2header(hash);
+	kh_destroy(ref, hash);
+	return header;
+}
+static inline uint8_t *alloc_data(bam1_t *b, int size)
+{
+	if (b->m_data < size) {
+		b->m_data = size;
+		kroundup32(b->m_data);
+		b->data = (uint8_t*)realloc(b->data, b->m_data);
+	}
+	return b->data;
+}
+static inline void parse_error(int64_t n_lines, const char * __restrict msg)
+{
+	fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
+	abort();
+}
+static inline void append_text(bam_header_t *header, kstring_t *str)
+{
+	size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
+	kroundup32(x); kroundup32(y);
+	if (x < y) 
+    {
+        header->n_text = y;
+        header->text = (char*)realloc(header->text, y);
+        if ( !header->text ) 
+        {
+            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
+            abort();
+        }
+    }
+    // Sanity check
+    if ( header->l_text+str->l+1 >= header->n_text )
+    {
+        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
+        abort();
+    }
+	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
+	header->l_text += str->l + 1;
+	header->text[header->l_text] = 0;
+}
+
+int sam_header_parse(bam_header_t *h)
+{
+	char **tmp;
+	int i;
+	free(h->target_len); free(h->target_name);
+	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
+	if (h->l_text < 3) return 0;
+	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
+	tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
+	if (h->n_targets == 0) return 0;
+	h->target_name = calloc(h->n_targets, sizeof(void*));
+	for (i = 0; i < h->n_targets; ++i)
+		h->target_name[i] = strdup(tmp[i]);
+	free(tmp);
+	tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
+	h->target_len = calloc(h->n_targets, 4);
+	for (i = 0; i < h->n_targets; ++i)
+		h->target_len[i] = atoi(tmp[i]);
+	free(tmp);
+	return h->n_targets;
+}
+
+bam_header_t *sam_header_read(tamFile fp)
+{
+	int ret, dret;
+	bam_header_t *header = bam_header_init();
+	kstring_t *str = fp->str;
+	while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+		str->s[str->l] = dret; // note that str->s is NOT null terminated!!
+		append_text(header, str);
+		if (dret != '\n') {
+			ret = ks_getuntil(fp->ks, '\n', str, &dret);
+			str->s[str->l] = '\n'; // NOT null terminated!!
+			append_text(header, str);
+		}
+		++fp->n_lines;
+	}
+	sam_header_parse(header);
+	bam_init_header_hash(header);
+	fp->is_first = 1;
+	return header;
+}
+
+int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
+{
+	int ret, doff, doff0, dret, z = 0;
+	bam1_core_t *c = &b->core;
+	kstring_t *str = fp->str;
+	kstream_t *ks = fp->ks;
+
+	if (fp->is_first) {
+		fp->is_first = 0;
+		ret = str->l;
+	} else {
+		do { // special consideration for empty lines
+			ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
+			if (ret >= 0) z += str->l + 1;
+		} while (ret == 0);
+	}
+	if (ret < 0) return -1;
+	++fp->n_lines;
+	doff = 0;
+
+	{ // name
+		c->l_qname = strlen(str->s) + 1;
+		memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
+		doff += c->l_qname;
+	}
+	{ // flag
+		long flag;
+		char *s;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		flag = strtol((char*)str->s, &s, 0);
+		if (*s) { // not the end of the string
+			flag = 0;
+			for (s = str->s; *s; ++s)
+				flag |= bam_char2flag_table[(int)*s];
+		}
+		c->flag = flag;
+	}
+	{ // tid, pos, qual
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
+		if (c->tid < 0 && strcmp(str->s, "*")) {
+			if (header->n_targets == 0) {
+				fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+				exit(1);
+			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+		}
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+		if (ret < 0) return -2;
+	}
+	{ // cigar
+		char *s, *t;
+		int i, op;
+		long x;
+		c->n_cigar = 0;
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
+		z += str->l + 1;
+		if (str->s[0] != '*') {
+			for (s = str->s; *s; ++s) {
+				if (isalpha(*s)) ++c->n_cigar;
+				else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
+			}
+			b->data = alloc_data(b, doff + c->n_cigar * 4);
+			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
+				x = strtol(s, &t, 10);
+				op = toupper(*t);
+				if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
+				else if (op == 'I') op = BAM_CINS;
+				else if (op == 'D') op = BAM_CDEL;
+				else if (op == 'N') op = BAM_CREF_SKIP;
+				else if (op == 'S') op = BAM_CSOFT_CLIP;
+				else if (op == 'H') op = BAM_CHARD_CLIP;
+				else if (op == 'P') op = BAM_CPAD;
+				else parse_error(fp->n_lines, "invalid CIGAR operation");
+				s = t + 1;
+				bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
+			}
+			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
+			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+			doff += c->n_cigar * 4;
+		} else {
+			if (!(c->flag&BAM_FUNMAP)) {
+				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+				c->flag |= BAM_FUNMAP;
+			}
+			c->bin = bam_reg2bin(c->pos, c->pos + 1);
+		}
+	}
+	{ // mtid, mpos, isize
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+		if (ret < 0) return -4;
+	}
+	{ // seq and qual
+		int i;
+		uint8_t *p = 0;
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
+		z += str->l + 1;
+		if (strcmp(str->s, "*")) {
+			c->l_qseq = strlen(str->s);
+			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
+				parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+			memset(p, 0, (c->l_qseq+1)/2);
+			for (i = 0; i < c->l_qseq; ++i)
+				p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+		} else c->l_qseq = 0;
+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
+		z += str->l + 1;
+		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
+			parse_error(fp->n_lines, "sequence and quality are inconsistent");
+		p += (c->l_qseq+1)/2;
+		if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+		else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+		doff += c->l_qseq + (c->l_qseq+1)/2;
+	}
+	doff0 = doff;
+	if (dret != '\n' && dret != '\r') { // aux
+		while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
+			uint8_t *s, type, key[2];
+			z += str->l + 1;
+			if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
+				parse_error(fp->n_lines, "missing colon in auxiliary data");
+			key[0] = str->s[0]; key[1] = str->s[1];
+			type = str->s[3];
+			s = alloc_data(b, doff + 3) + doff;
+			s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
+			if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
+				s = alloc_data(b, doff + 2) + doff;
+				*s++ = 'A'; *s = str->s[5];
+				doff += 2;
+			} else if (type == 'I' || type == 'i') {
+				long long x;
+				s = alloc_data(b, doff + 5) + doff;
+				x = (long long)atoll(str->s + 5);
+				if (x < 0) {
+					if (x >= -127) {
+						*s++ = 'c'; *(int8_t*)s = (int8_t)x;
+						s += 1; doff += 2;
+					} else if (x >= -32767) {
+						*s++ = 's'; *(int16_t*)s = (int16_t)x;
+						s += 2; doff += 3;
+					} else {
+						*s++ = 'i'; *(int32_t*)s = (int32_t)x;
+						s += 4; doff += 5;
+						if (x < -2147483648ll)
+							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
+									(long long)fp->n_lines, x);
+					}
+				} else {
+					if (x <= 255) {
+						*s++ = 'C'; *s++ = (uint8_t)x;
+						doff += 2;
+					} else if (x <= 65535) {
+						*s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
+						s += 2; doff += 3;
+					} else {
+						*s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
+						s += 4; doff += 5;
+						if (x > 4294967295ll)
+							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
+									(long long)fp->n_lines, x);
+					}
+				}
+			} else if (type == 'f') {
+				s = alloc_data(b, doff + 5) + doff;
+				*s++ = 'f';
+				*(float*)s = (float)atof(str->s + 5);
+				s += 4; doff += 5;
+			} else if (type == 'd') {
+				s = alloc_data(b, doff + 9) + doff;
+				*s++ = 'd';
+				*(float*)s = (float)atof(str->s + 9);
+				s += 8; doff += 9;
+			} else if (type == 'Z' || type == 'H') {
+				int size = 1 + (str->l - 5) + 1;
+				if (type == 'H') { // check whether the hex string is valid
+					int i;
+					if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
+					for (i = 0; i < str->l - 5; ++i) {
+						int c = toupper(str->s[5 + i]);
+						if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
+							parse_error(fp->n_lines, "invalid hex character");
+					}
+				}
+				s = alloc_data(b, doff + size) + doff;
+				*s++ = type;
+				memcpy(s, str->s + 5, str->l - 5);
+				s[str->l - 5] = 0;
+				doff += size;
+			} else if (type == 'B') {
+				int32_t n = 0, Bsize, k = 0, size;
+				char *p;
+				if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+				Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+				for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+					if (*p == ',') ++n;
+				p = str->s + 7; // now p points to the first number in the array
+				size = 6 + Bsize * n; // total number of bytes allocated to this tag
+				s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+				*s++ = 'B'; *s++ = str->s[5];
+				memcpy(s, &n, 4); s += 4; // write the number of elements
+				if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
+				else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
+				else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
+				else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+				else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
+				else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+				else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtof(p, &p),       ++p;
+				else parse_error(fp->n_lines, "unrecognized array type");
+				s += Bsize * n; doff += size;
+			} else parse_error(fp->n_lines, "unrecognized type");
+			if (dret == '\n' || dret == '\r') break;
+		}
+	}
+	b->l_aux = doff - doff0;
+	b->data_len = doff;
+	return z;
+}
+
+tamFile sam_open(const char *fn)
+{
+	tamFile fp;
+	gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
+	if (gzfp == 0) return 0;
+	fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
+	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
+	fp->fp = gzfp;
+	fp->ks = ks_init(fp->fp);
+	return fp;
+}
+
+void sam_close(tamFile fp)
+{
+	if (fp) {
+		ks_destroy(fp->ks);
+		gzclose(fp->fp);
+		free(fp->str->s); free(fp->str);
+		free(fp);
+	}
+}