/*

bam_index_subset.h

This file contains an unmodified subset of the contents of
'bam_index.c' from samtools 0.1.8.

Note this is not a true header file. The assumption is that it is
included no more than once per namespace.


########## License:

The MIT License

Copyright (c) 2008-2009 Genome Research Ltd.

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.


########## Additional notice for CASAVA installation:

This file [bam_index_subset.h] in the CASAVA installation has been
copied from the file [bam_index.c] in the SAMtools package and
modified by Illumina as permitted under the MIT license that governs
SAMtools. The terms of the MIT license specify your right to further
modify and distribute the SAMtools code. For the avoidance of doubt,
your rights with respect to copying, modifying, using and distributing
CASAVA are more restricted than the rights in the MIT license, and are
set forth in the Illumina Genome Analyzer Software License Agreement
and the Illumina Source Code License Agreement.

*/

#include "khash.h"
#include "ksort.h"

// 1<<14 is the size of minimum bin.
#define BAM_LIDX_SHIFT    14

#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1

typedef struct {
	uint64_t u, v;
} pair64_t;

#define pair64_lt(a,b) ((a).u < (b).u)
KSORT_INIT(off, pair64_t, pair64_lt)

typedef struct {
	uint32_t m, n;
	pair64_t *list;
} bam_binlist_t;

typedef struct {
	int32_t n, m;
	uint64_t *offset;
} bam_lidx_t;

KHASH_MAP_INIT_INT(i, bam_binlist_t)

struct __bam_index_t {
	int32_t n;
	uint64_t n_no_coor; // unmapped reads without coordinate
	khash_t(i) **index;
	bam_lidx_t *index2;
};

static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_MAX_BIN])
{
	int i = 0, k;
	if (beg >= end) return 0;
	if (end >= 1u<<29) end = 1u<<29;
	--end;
	list[i++] = 0;
	for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) list[i++] = k;
	for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) list[i++] = k;
	for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) list[i++] = k;
	for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) list[i++] = k;
	for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
	return i;
}

static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
{
	uint32_t rbeg = b->core.pos;
	uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
	return (rend > beg && rbeg < end);
}