/*
 * inc/Sam_view.h
 * 
 * Copyright (c) 2011-2013 BGI-Shenzhen <soap at genomics dot org dot cn>. 
 *
 * This file is part of SOAPdenovo-Trans.
 *
 * SOAPdenovo-Trans is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo-Trans is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo-Trans.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifndef SAM_VIEW_H
#define SAM_VIEW_H


static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
static char *g_library, *g_rg;
static int g_sol2sanger_tbl[128];

static void sol2sanger(bam1_t *b)
{
	int l;
	uint8_t *qual = bam1_qual(b);
	if (g_sol2sanger_tbl[30] == 0) {
		for (l = 0; l != 128; ++l) {
			g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
			if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
		}
	}
	for (l = 0; l < b->core.l_qseq; ++l) {
		int q = qual[l];
		if (q > 127) q = 127;
		qual[l] = g_sol2sanger_tbl[q];
	}
}

static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
{
	if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
		return 1;
	if (g_rg) {
		uint8_t *s = bam_aux_get(b, "RG");
		if (s && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
	}
	if (g_library) {
		const char *p = bam_get_library((bam_header_t*)h, b);
		return (p && strcmp(p, g_library) == 0)? 0 : 1;
	}
	return 0;
}


#endif