--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/misc/ace2sam.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,249 @@
+/* The MIT License
+
+   Copyright (c) 2011  Heng Li <lh3@live.co.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 <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+#include "kstring.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define N_TMPSTR 5
+#define LINE_LEN 60
+
+// append a CIGAR operation plus length
+#define write_cigar(_c, _n, _m, _v) do { \
+		if (_n == _m) { \
+			_m = _m? _m<<1 : 4; \
+			_c = realloc(_c, _m * sizeof(unsigned)); \
+		} \
+		_c[_n++] = (_v); \
+	} while (0)
+
+// a fatal error
+static void fatal(const char *msg)
+{
+	fprintf(stderr, "E %s\n", msg);
+	exit(1);
+}
+// remove pads
+static void remove_pads(const kstring_t *src, kstring_t *dst)
+{
+	int i, j;
+	dst->l = 0;
+	kputsn(src->s, src->l, dst);
+	for (i = j = 0; i < dst->l; ++i)
+		if (dst->s[i] != '*') dst->s[j++] = dst->s[i];
+	dst->s[j] = 0;
+	dst->l = j;
+}
+
+int main(int argc, char *argv[])
+{
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t s, t[N_TMPSTR];
+	int dret, i, k, af_n, af_max, af_i, c, is_padded = 0, write_cns = 0, *p2u = 0;
+	long m_cigar = 0, n_cigar = 0;
+	unsigned *af, *cigar = 0;
+
+	while ((c = getopt(argc, argv, "pc")) >= 0) {
+		switch (c) {
+			case 'p': is_padded = 1; break;
+			case 'c': write_cns = 1; break;
+		}
+	}
+	if (argc == optind) {
+		fprintf(stderr, "\nUsage:   ace2sam [-pc] <in.ace>\n\n");
+		fprintf(stderr, "Options: -p     output padded SAM\n");
+		fprintf(stderr, "         -c     write the contig sequence in SAM\n\n");
+		fprintf(stderr, "Notes: 1. Fields must appear in the following order: (CO->[BQ]->(AF)->(RD->QA))\n");
+		fprintf(stderr, "       2. The order of reads in AF and in RD must be identical\n");
+		fprintf(stderr, "       3. Except in BQ, words and numbers must be separated by a single SPACE or TAB\n");
+		fprintf(stderr, "       4. This program writes the headerless SAM to stdout and header to stderr\n\n");
+		return 1;
+	}
+
+	s.l = s.m = 0; s.s = 0;
+	af_n = af_max = af_i = 0; af = 0;
+	for (i = 0; i < N_TMPSTR; ++i) t[i].l = t[i].m = 0, t[i].s = 0;
+	fp = strcmp(argv[1], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+		if (strcmp(s.s, "CO") == 0) { // contig sequence
+			kstring_t *cns;
+			t[0].l = t[1].l = t[2].l = t[3].l = t[4].l = 0; // 0: name; 1: padded ctg; 2: unpadded ctg/padded read; 3: unpadded read; 4: SAM line
+			af_n = af_i = 0; // reset the af array
+			ks_getuntil(ks, 0, &s, &dret); kputs(s.s, &t[0]); // contig name
+			ks_getuntil(ks, '\n', &s, &dret); // read the whole line
+			while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputsn(s.s, s.l, &t[1]); // read the padded consensus sequence
+			remove_pads(&t[1], &t[2]); // construct the unpadded sequence
+			// compute the array for mapping padded positions to unpadded positions
+			p2u = realloc(p2u, t[1].m * sizeof(int));
+			for (i = k = 0; i < t[1].l; ++i) {
+				p2u[i] = k;
+				if (t[1].s[i] != '*') ++k;
+			}
+			// write out the SAM header and contig sequences
+			fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
+			cns = &t[is_padded?1:2];
+			fprintf(stderr, "S >%s\n", t[0].s);
+			for (i = 0; i < cns->l; i += LINE_LEN) {
+				fputs("S ", stderr);
+				for (k = 0; k < LINE_LEN && i + k < cns->l; ++k)
+					fputc(cns->s[i + k], stderr);
+				fputc('\n', stderr);
+			}
+
+#define __padded2cigar(sp) do { \
+		int i, l_M = 0, l_D = 0; \
+		for (i = 0; i < sp.l; ++i) { \
+			if (sp.s[i] == '*') { \
+				if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+				++l_D; l_M = 0; \
+			} else { \
+				if (l_D) write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+				++l_M; l_D = 0; \
+			} \
+		} \
+		if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+		else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+	} while (0)
+
+			if (write_cns) { // write the consensus SAM line (dummy read)
+				n_cigar = 0;
+				if (is_padded) __padded2cigar(t[1]);
+				else write_cigar(cigar, n_cigar, m_cigar, t[2].l<<4);
+				kputsn(t[0].s, t[0].l, &t[4]); kputs("\t516\t", &t[4]); kputsn(t[0].s, t[0].l, &t[4]); kputs("\t1\t60\t", &t[4]);
+				for (i = 0; i < n_cigar; ++i) {
+					kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
+				}
+				kputs("\t*\t0\t0\t", &t[4]); kputsn(t[2].s, t[2].l, &t[4]); kputs("\t*", &t[4]);
+			}
+		} else if (strcmp(s.s, "BQ") == 0) { // contig quality
+			if (t[0].l == 0) fatal("come to 'BQ' before reading 'CO'");
+			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire "BQ" line
+			if (write_cns) t[4].s[--t[4].l] = 0; // remove the trailing "*"
+			for (i = 0; i < t[2].l; ++i) { // read the consensus quality
+				int q;
+				if (ks_getuntil(ks, 0, &s, &dret) < 0) fprintf(stderr, "E truncated contig quality\n");
+				if (s.l) {
+					q = atoi(s.s) + 33;
+					if (q > 126) q = 126;
+					if (write_cns) kputc(q, &t[4]);
+				} else --i;
+			}
+			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+			ks_getuntil(ks, '\n', &s, &dret); // skip the empty line
+			if (write_cns) puts(t[4].s); t[4].l = 0;
+		} else if (strcmp(s.s, "AF") == 0) { // padded read position
+			int reversed, neg, pos;
+			if (t[0].l == 0) fatal("come to 'AF' before reading 'CO'");
+			if (write_cns) {
+				if (t[4].l) puts(t[4].s);
+				t[4].l = 0;
+			}
+			ks_getuntil(ks, 0, &s, &dret); // read name
+			ks_getuntil(ks, 0, &s, &dret); reversed = s.s[0] == 'C'? 1 : 0; // strand
+			ks_getuntil(ks, 0, &s, &dret); pos = atoi(s.s); neg = pos < 0? 1 : 0; pos = pos < 0? -pos : pos; // position
+			if (af_n == af_max) { // double the af array
+				af_max = af_max? af_max<<1 : 4;
+				af = realloc(af, af_max * sizeof(unsigned));
+			}
+			af[af_n++] = pos << 2 | neg << 1 | reversed; // keep the placement information
+		} else if (strcmp(s.s, "RD") == 0) { // read sequence
+			if (af_i >= af_n) fatal("more 'RD' records than 'AF'");
+			t[2].l = t[3].l = t[4].l = 0;
+			ks_getuntil(ks, 0, &t[4], &dret); // QNAME
+			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire RD line
+			while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputs(s.s, &t[2]); // read the read sequence
+		} else if (strcmp(s.s, "QA") == 0) { // clipping
+			if (af_i >= af_n) fatal("more 'QA' records than 'AF'");
+			int beg, end, pos, op;
+			ks_getuntil(ks, 0, &s, &dret); ks_getuntil(ks, 0, &s, &dret); // skip quality clipping
+			ks_getuntil(ks, 0, &s, &dret); beg = atoi(s.s) - 1; // align clipping start
+			ks_getuntil(ks, 0, &s, &dret); end = atoi(s.s); // clipping end
+			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+			// compute 1-based POS
+			pos = af[af_i]>>2; // retrieve the position information
+			if (af[af_i]>>1&1) pos = -pos;
+			pos += beg; // now pos is the true padded position
+			// generate CIGAR
+			remove_pads(&t[2], &t[3]); // backup the unpadded read sequence
+			n_cigar = 0;
+			if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4);
+			if (is_padded) {
+				__padded2cigar(t[2]);
+				if (beg && n_cigar > 1) cigar[1] -= beg<<4; // fix the left-hand CIGAR 
+				if (end < t[2].l && n_cigar) cigar[n_cigar-1] -= (t[2].l - end)<<4; // fix the right-hand CIGAR
+			} else {
+				// generate flattened CIGAR string
+				for (i = beg, k = pos - 1; i < end; ++i, ++k)
+					t[2].s[i] = t[2].s[i] != '*'? (t[1].s[k] != '*'? 0 : 1) : (t[1].s[k] != '*'? 2 : 6);
+				// generate the proper CIGAR
+				for (i = beg + 1, k = 1, op = t[2].s[beg]; i < end; ++i) {
+					if (op != t[2].s[i]) {
+						write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
+						op = t[2].s[i]; k = 1;
+					} else ++k;
+				}
+				write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
+				// remove unnecessary "P" and possibly merge adjacent operations
+				for (i = 2; i < n_cigar; ++i) {
+					if ((cigar[i]&0xf) != 1 && (cigar[i-1]&0xf) == 6 && (cigar[i-2]&0xf) != 1) {
+						cigar[i-1] = 0;
+						if ((cigar[i]&0xf) == (cigar[i-2]&0xf)) // merge operations
+							cigar[i] += cigar[i-2], cigar[i-2] = 0;
+					}
+				}
+				for (i = k = 0; i < n_cigar; ++i) // squeeze out dumb operations
+					if (cigar[i]) cigar[k++] = cigar[i];
+				n_cigar = k;
+			}
+			if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l - end)<<4|4);
+			// write the SAM line for the read
+			kputc('\t', &t[4]); // QNAME has already been written
+			kputw((af[af_i]&1)? 16 : 0, &t[4]); kputc('\t', &t[4]); // FLAG
+			kputsn(t[0].s, t[0].l, &t[4]); kputc('\t', &t[4]); // RNAME
+			kputw(is_padded? pos : p2u[pos-1]+1, &t[4]); // POS
+			kputs("\t60\t", &t[4]); // MAPQ
+			for (i = 0; i < n_cigar; ++i) { // CIGAR
+				kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
+			}
+			kputs("\t*\t0\t0\t", &t[4]); // empty MRNM, MPOS and TLEN
+			kputsn(t[3].s, t[3].l, &t[4]); // unpadded SEQ
+			kputs("\t*", &t[4]); // QUAL
+			puts(t[4].s); // print to stdout
+			++af_i;
+		} else if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	free(af); free(s.s); free(cigar); free(p2u);
+	for (i = 0; i < N_TMPSTR; ++i) free(t[i].s);
+	return 0;
+}