--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/padding.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,479 @@
+#include <string.h>
+#include <assert.h>
+#include <unistd.h>
+#include "kstring.h"
+#include "sam_header.h"
+#include "sam.h"
+#include "bam.h"
+#include "faidx.h"
+
+bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/
+
+static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
+{
+	if (n != b->core.n_cigar) {
+		int o = b->core.l_qname + b->core.n_cigar * 4;
+		if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
+			b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
+			kroundup32(b->m_data);
+			b->data = (uint8_t*)realloc(b->data, b->m_data);
+		}
+		memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
+		memcpy(b->data + b->core.l_qname, cigar, n * 4);
+		b->data_len += (n - b->core.n_cigar) * 4;
+		b->core.n_cigar = n;
+	} else memcpy(b->data + b->core.l_qname, cigar, n * 4);
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+		if (_n == _m) { \
+			_m = _m? _m<<1 : 4; \
+			_c = (uint32_t*)realloc(_c, _m * 4); \
+		} \
+		_c[_n++] = (_v); \
+	} while (0)
+
+static void unpad_seq(bam1_t *b, kstring_t *s)
+{
+	int k, j, i;
+	int length;
+	uint32_t *cigar = bam1_cigar(b);
+	uint8_t *seq = bam1_seq(b);
+	// b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+	// We need the padded length after alignment from the CIGAR (excluding
+	// soft clips S, but including pads from CIGAR D operations)
+	length = 0;
+	for (k = 0; k < b->core.n_cigar; ++k) {
+		int op, ol;
+		op= bam_cigar_op(cigar[k]);
+		ol = bam_cigar_oplen(cigar[k]);
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
+			length += ol;
+	}
+	ks_resize(s, length);
+	for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+		int op, ol;
+		op = bam_cigar_op(cigar[k]);
+		ol = bam_cigar_oplen(cigar[k]);
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+			for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
+		} else if (op == BAM_CSOFT_CLIP) {
+			j += ol;
+		} else if (op == BAM_CHARD_CLIP) {
+			/* do nothing */
+		} else if (op == BAM_CDEL) {
+			for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+                } else {
+			fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                        assert(-1);
+		}
+	}
+	assert(length == s->l);
+}
+
+int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
+{
+	char base;
+	char *fai_ref = 0;
+	int fai_ref_len = 0, k;
+
+	fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+	if (fai_ref_len != ref_len) {
+		fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
+		free(fai_ref);
+		return -1;
+	}
+	ks_resize(seq, ref_len);
+	seq->l = 0;
+	for (k = 0; k < ref_len; ++k) {
+		base = fai_ref[k];
+		if (base == '-' || base == '*') {
+			// Map gaps to null to match unpad_seq function
+			seq->s[seq->l++] = 0;
+		} else {
+			int i = bam_nt16_table[(int)base];
+			if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+				fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
+				free(fai_ref);
+				return -1;
+			}
+			seq->s[seq->l++] = i;
+		}
+	}
+	assert(ref_len == seq->l);
+	free(fai_ref);
+	return 0;
+}
+
+int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len)
+{
+	char base;
+	char *fai_ref = 0;
+	int fai_ref_len = 0, k;
+	int bases=0, gaps=0;
+
+	fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+	if (fai_ref_len != padded_len) {
+		fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len);
+		free(fai_ref);
+		return -1;
+	}
+	for (k = 0; k < padded_len; ++k) {
+		//fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+		base = fai_ref[k];
+		if (base == '-' || base == '*') {
+			gaps += 1;
+		} else {
+			int i = bam_nt16_table[(int)base];
+			if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+				fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
+				free(fai_ref);
+				return -1;
+			}
+			bases += 1;
+		}
+	}
+	free(fai_ref);
+	assert (padded_len == bases + gaps);
+	return bases;
+}
+
+inline int * update_posmap(int *posmap, kstring_t ref)
+{
+	int i, k;
+	posmap = realloc(posmap, ref.m * sizeof(int));
+	for (i = k = 0; i < ref.l; ++i) {
+		posmap[i] = k;
+		if (ref.s[i]) ++k;
+	}
+	return posmap;
+}
+
+int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
+{
+	bam_header_t *h = 0;
+	bam1_t *b = 0;
+	kstring_t r, q;
+	int r_tid = -1;
+	uint32_t *cigar2 = 0;
+	int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
+
+	b = bam_init1();
+	r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+	int read_ret;
+	h = in->header;
+	while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
+		uint32_t *cigar = bam1_cigar(b);
+		n2 = 0;
+		if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
+			// fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
+			r_tid = b->core.tid;
+			unpad_seq(b, &r);
+			if (h->target_len[r_tid] != r.l) {
+				fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+				return -1;
+			}
+			if (fai) {
+				// Check the embedded reference matches the FASTA file
+				if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
+					fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
+					return -1;
+				}
+				assert(r.l == q.l);
+				int i;
+				for (i = 0; i < r.l; ++i) {
+					if (r.s[i] != q.s[i]) {
+						// Show gaps as ASCII 45
+						fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+							h->target_name[b->core.tid], i+1,
+							r.s[i] ? bam_nt16_rev_table[(int)r.s[i]] : 45,
+							q.s[i] ? bam_nt16_rev_table[(int)q.s[i]] : 45);
+						return -1;
+					}
+				}
+			}
+			write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
+			replace_cigar(b, n2, cigar2);
+			posmap = update_posmap(posmap, r);
+		} else if (b->core.n_cigar > 0) {
+			int i, k, op;
+			if (b->core.tid < 0) {
+				fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b));
+				return -1;
+			} else if (b->core.tid == r_tid) {
+				; // good case, reference available
+				//fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
+			} else if (fai) {
+				if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+					fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+					return -1;
+				}
+				posmap = update_posmap(posmap, r);
+				r_tid = b->core.tid;
+				// fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+			} else {				
+				fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
+				return -1;
+			}
+			unpad_seq(b, &q);
+			if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+			} else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[1]);
+				}
+			}
+			/* Determine CIGAR operator for each base in the aligned read */
+			for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
+				q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+			/* Include any pads if starts with an insert */
+			if (q.s[0] == BAM_CINS) {
+				for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+				if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+			}
+			/* Count consecutive CIGAR operators to turn into a CIGAR string */
+			for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
+				if (op != q.s[i]) {
+					write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+					op = q.s[i]; k = 1;
+				} else ++k;
+			}
+			write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+			if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+                        } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+			  	}
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+			}
+			/* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+			int pre_op, post_op;
+			for (i = 2; i < n2; ++i)
+				if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+					pre_op = bam_cigar_op(cigar2[i-2]);
+					post_op = bam_cigar_op(cigar2[i]);
+					/* Note don't need to check for X/= as code above will use M only */
+					if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+						/* This is a redundant P operator */
+						cigar2[i-1] = 0; // i.e. 0M
+						/* If had same operator either side, combine them in post_op */
+						if (pre_op == post_op) {
+							/* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+							cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+							cigar2[i-2] = 0; // i.e. 0M
+						}
+					}
+				}
+			/* Remove the zero'd operators (0M) */
+			for (i = k = 0; i < n2; ++i)
+				if (cigar2[i]) cigar2[k++] = cigar2[i];
+			n2 = k;
+			replace_cigar(b, n2, cigar2);
+			b->core.pos = posmap[b->core.pos];
+			if (b->core.mtid < 0 || b->core.mpos < 0) {
+				/* Nice case, no mate to worry about*/
+				// fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+				/* TODO - Warning if FLAG says mate should be mapped? */
+				/* Clean up funny input where mate position is given but mate reference is missing: */
+				b->core.mtid = -1;
+				b->core.mpos = -1;
+			} else if (b->core.mtid == b->core.tid) {
+				/* Nice case, same reference */
+				// fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+				b->core.mpos = posmap[b->core.mpos];
+			} else {
+				/* Nasty case, Must load alternative posmap */
+				// fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+				if (!fai) {
+					fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+					return -1;
+				}
+				/* Temporarily load the other reference sequence */
+				if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+					fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+					return -1;
+				}
+				posmap = update_posmap(posmap, r);
+				b->core.mpos = posmap[b->core.mpos];
+				/* Restore the reference and posmap*/
+				if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+					fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+					return -1;
+				}
+				posmap = update_posmap(posmap, r);
+			}
+		}
+		samwrite(out, b);
+	}
+	if (read_ret < -1) {
+		fprintf(stderr, "[depad] truncated file.\n");
+		ret = 1;
+	}
+	free(r.s); free(q.s); free(posmap);
+	bam_destroy1(b);
+	return ret;
+}
+
+bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
+{
+	int i = 0, unpadded_len = 0;
+	bam_header_t *header = 0 ;
+
+	header = bam_header_dup(old);
+	for (i = 0; i < old->n_targets; ++i) {
+		unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
+		if (unpadded_len < 0) {
+			fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
+		} else {
+			header->target_len[i] = unpadded_len;
+			//fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+		}
+	}
+	/* Duplicating the header allocated new buffer for header string */
+	/* After modifying the @SQ lines it will only get smaller, since */
+	/* the LN entries will be the same or shorter, and we'll remove */
+	/* any MD entries (MD5 checksums). */
+	assert(strlen(old->text) == strlen(header->text));
+	assert (0==strcmp(old->text, header->text));
+	const char *text;
+	text = old->text;
+	header->text[0] = '\0'; /* Resuse the allocated buffer */
+	char * newtext = header->text;
+	char * end=NULL;
+	while (text[0]=='@') {
+		end = strchr(text, '\n');
+		assert(end != 0);
+		if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') {
+			/* TODO - edit the @SQ line here to remove MD and fix LN. */
+			/* For now just remove the @SQ line, and samtools will */
+			/* automatically generate a minimal replacement with LN. */
+			/* However, that discards any other tags like AS, SP, UR. */
+			//fprintf(stderr, "[depad] Removing @SQ line\n");
+		} else {
+			/* Copy this line to the new header */
+			strncat(newtext, text, end - text + 1);
+		}
+		text = end + 1;
+	}
+	assert (text[0]=='\0');
+	/* Check we didn't overflow the buffer */
+	assert (strlen(header->text) <= strlen(old->text));
+	if (strlen(header->text) < header->l_text) {
+		//fprintf(stderr, "[depad] Reallocating header buffer\n");
+		assert (newtext == header->text);
+		newtext = malloc(strlen(header->text) + 1);
+		strcpy(newtext, header->text);
+		free(header->text);
+		header->text = newtext;
+		header->l_text = strlen(newtext);
+	}
+	//fprintf(stderr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text);
+	return header;
+}
+
+static int usage(int is_long_help);
+
+int main_pad2unpad(int argc, char *argv[])
+{
+	samfile_t *in = 0, *out = 0;
+        bam_header_t *h = 0;
+	faidx_t *fai = 0;
+	int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
+	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
+        int ret=0;
+
+	/* parse command-line options */
+	strcpy(in_mode, "r"); strcpy(out_mode, "w");
+	while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
+		switch (c) {
+		case 'S': is_bamin = 0; break;
+		case 's': assert(compress_level == -1); is_bamout = 0; break;
+		case 'o': fn_out = strdup(optarg); break;
+		case 'u': assert(is_bamout == 1); compress_level = 0; break;
+		case '1': assert(is_bamout == 1); compress_level = 1; break;
+		case 'T': fn_ref = strdup(optarg); break;
+                case '?': is_long_help = 1; break;
+		default: return usage(is_long_help);
+		}
+        }
+	if (argc == optind) return usage(is_long_help);
+
+	if (is_bamin) strcat(in_mode, "b");
+	if (is_bamout) strcat(out_mode, "b");
+	strcat(out_mode, "h");
+	if (compress_level >= 0) {
+		char tmp[2];
+		tmp[0] = compress_level + '0'; tmp[1] = '\0';
+		strcat(out_mode, tmp);
+	}
+
+	// Load FASTA reference (also needed for SAM -> BAM if missing header)
+	if (fn_ref) {
+		fn_list = samfaipath(fn_ref);
+		fai = fai_load(fn_ref);
+	}
+	// open file handlers
+	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
+		fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
+		ret = 1;
+		goto depad_end;
+	}
+	if (in->header == 0) {
+		fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
+		ret = 1;
+		goto depad_end;
+	}
+	if (in->header->text == 0 || in->header->l_text == 0) {
+		fprintf(stderr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
+		assert (0 == in->header->l_text);
+		assert (0 == in->header->text);
+	}
+	if (fn_ref) {
+		h = fix_header(in->header, fai);
+	} else {
+		fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+		h = in->header;
+	}
+	if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
+		fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+		ret = 1;
+		goto depad_end;
+	}
+
+	// Do the depad
+	ret = bam_pad2unpad(in, out, fai);
+
+depad_end:
+	// close files, free and return
+	if (fai) fai_destroy(fai);
+	if (h != in->header) bam_header_destroy(h);
+	samclose(in);
+	samclose(out);
+	free(fn_list); free(fn_out);
+	return ret;
+}
+
+static int usage(int is_long_help)
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Usage:   samtools depad <in.bam>\n\n");
+	fprintf(stderr, "Options: -s       output is SAM (default is BAM)\n");
+	fprintf(stderr, "         -S       input is SAM (default is BAM)\n");
+	fprintf(stderr, "         -u       uncompressed BAM output (can't use with -s)\n");
+	fprintf(stderr, "         -1       fast compression BAM output (can't use with -s)\n");
+	fprintf(stderr, "         -T FILE  reference sequence file [null]\n");
+	fprintf(stderr, "         -o FILE  output file name [stdout]\n");
+	fprintf(stderr, "         -?       longer help\n");
+	fprintf(stderr, "\n");
+	if (is_long_help)
+		fprintf(stderr, "Notes:\n\
+\n\
+  1. Requires embedded reference sequences (before the reads for that reference),\n\
+     with the future aim to also support a FASTA padded reference sequence file.\n\
+\n\
+  2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
+\n");
+        return 1;
+}