/*  bam.c -- BAM format.

 Copyright (C) 2008-2013, 2015 Genome Research Ltd.
 Portions copyright (C) 2009-2012 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 <config.h>

#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include "bam.h"
#include <htslib/kstring.h>
#include "sam_header.h"

char *bam_format1(const bam_header_t *header, const bam1_t *b)
{
	kstring_t str;
	str.l = str.m = 0; str.s = NULL;
	if (sam_format1(header, b, &str) < 0) {
		free(str.s);
		str.s = NULL;
		return NULL;
	}
	return str.s;
}

// int bam_view1(const bam_header_t *header, const bam1_t *b)
// {
// 	char *s = bam_format1(header, b);
// 	int ret = -1;
// 	if (!s) return -1;
// 	if (puts(s) != EOF) ret = 0;
// 	free(s);
// 	return ret;
// }

int bam_validate1(const bam_header_t *header, const bam1_t *b)
{
	char *s;

	if (b->core.tid < -1 || b->core.mtid < -1) return 0;
	if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;

	if (b->data_len < b->core.l_qname) return 0;
	s = memchr(bam1_qname(b), '\0', b->core.l_qname);
	if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;

	// FIXME: Other fields could also be checked, especially the auxiliary data

	return 1;
}

#ifndef MIN
#define MIN(a,b) ((a)<(b)?(a):(b))
#endif

// FIXME: we should also check the LB tag associated with each alignment
const char *bam_get_library(bam_header_t *h, const bam1_t *b)
{
	// Slow and inefficient.  Rewrite once we get a proper header API.
	const char *rg;
	char *cp = h->text;
	rg = (char *)bam_aux_get(b, "RG");

	if (!rg)
		return NULL;
	else
		rg++;

	// Header is guaranteed to be nul terminated, so this is valid.
	while (*cp) {
		char *ID, *LB;
		char last = '\t';

		// Find a @RG line
		if (strncmp(cp, "@RG", 3) != 0) {
			while (*cp && *cp != '\n') cp++; // skip line
			if (*cp) cp++;
			continue;
		}

		// Find ID: and LB: keys
		cp += 4;
		ID = LB = NULL;
		while (*cp && *cp != '\n') {
			if (last == '\t') {
				if (strncmp(cp, "LB:", 3) == 0)
					LB = cp+3;
				else if (strncmp(cp, "ID:", 3) == 0)
					ID = cp+3;
			}
			last = *cp++;
		}

		if (!ID || !LB)
			continue;

		// Check it's the correct ID
		if (strncmp(rg, ID, strlen(rg)) != 0 || ID[strlen(rg)] != '\t')
			continue;

		// Valid until next query
		static char LB_text[1024];
		for (cp = LB; *cp && *cp != '\t' && *cp != '\n'; cp++)
			;
		strncpy(LB_text, LB, MIN(cp-LB, 1023));
		LB_text[MIN(cp-LB, 1023)] = 0;

		// Return it; valid until the next query.
		return LB_text;
	}

	return NULL;
}

int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
{
	int ret;
	bam_iter_t iter;
	bam1_t *b;
	b = bam_init1();
	iter = bam_iter_query(idx, tid, beg, end);
	while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
	bam_iter_destroy(iter);
	bam_destroy1(b);
	return (ret == -1)? 0 : ret;
}

/************
 * Remove B *
 ************/

#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )

int bam_remove_B(bam1_t *b)
{
	int i, j, end_j, k, l, no_qual;
	uint32_t *cigar, *new_cigar;
	uint8_t *seq, *qual, *p;
	// test if removal is necessary
	if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
	cigar = bam1_cigar(b);
	for (k = 0; k < b->core.n_cigar; ++k)
		if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
	if (k == b->core.n_cigar) return 0; // no 'B'
	if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
	// allocate memory for the new CIGAR
	if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
		b->m_data = b->data_len + b->core.n_cigar * 4;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
		cigar = bam1_cigar(b); // after realloc, cigar may be changed
	}
	new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
	// the core loop
	seq = bam1_seq(b); qual = bam1_qual(b);
	no_qual = (qual[0] == 0xff); // test whether base quality is available
	i = j = 0; end_j = -1;
	for (k = l = 0; k < b->core.n_cigar; ++k) {
		int op  = bam_cigar_op(cigar[k]);
		int len = bam_cigar_oplen(cigar[k]);
		if (op == BAM_CBACK) { // the backward operation
			int t, u;
			if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
			if (len > j) goto rmB_err; // an excessively long backward
			for (t = l - 1, u = 0; t >= 0; --t) { // look back
				int op1  = bam_cigar_op(new_cigar[t]);
				int len1 = bam_cigar_oplen(new_cigar[t]);
				if (bam_cigar_type(op1)&1) { // consume the query
					if (u + len1 >= len) { // stop
						new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
						break;
					} else u += len1;
				}
			}
			if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
			l = t + 1;
			end_j = j; j -= len;
		} else { // other CIGAR operations
			new_cigar[l++] = cigar[k];
			if (bam_cigar_type(op)&1) { // consume the query
				if (i != j) { // no need to copy if i == j
					int u, c, c0;
					for (u = 0; u < len; ++u) { // construct the consensus
						c = bam1_seqi(seq, i+u);
						if (j + u < end_j) { // in an overlap
							c0 = bam1_seqi(seq, j+u);
							if (c != c0) { // a mismatch; choose the better base
								if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
									bam1_seq_seti(seq, j+u, c);
									qual[j+u] = qual[i+u] - qual[j+u];
								} else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
							} else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
						} else { // not in an overlap; copy over
							bam1_seq_seti(seq, j+u, c);
							qual[j+u] = qual[i+u];
						}
					}
				}
				i += len, j += len;
			}
		}
	}
	if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
	// merge adjacent operations if possible
	for (k = 1; k < l; ++k)
		if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
			new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
	// kill zero length operations
	for (k = i = 0; k < l; ++k)
		if (new_cigar[k] >> BAM_CIGAR_SHIFT)
			new_cigar[i++] = new_cigar[k];
	l = i;
	// update b
	memcpy(cigar, new_cigar, l * 4); // set CIGAR
	p = b->data + b->core.l_qname + l * 4;
	memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
	memmove(p, qual, j); p += j; // set QUAL
	memmove(p, bam1_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields
	b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
	b->data_len = p - b->data; // update record length
	return 0;

rmB_err:
	b->core.flag |= BAM_FUNMAP;
	return -1;
}
