// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file
///
/// \author Chris Saunders
///

///
/// This code demonstrates a very simple parse of the bam index (bai) file to 
/// discover what reference indexes are present. Note the error checking is
/// very incomplete.
///

#include <stdint.h>

#include <cassert>
#include <cstdio>
#include <cstdlib>
#include <cstring>

#include <vector>


int main(int argc, char **argv) {

    const char* prog_name(argv[0]);

    if(argc != 2){
        fprintf(stderr,"usage: %s bai_file\n",prog_name);
        exit(EXIT_FAILURE);
    }

    const char* bai_name(argv[1]);

    FILE* fp(fopen(bai_name,"rb"));
    if(fp == NULL) { 
        fprintf(stderr,"Can't open bai_file: %s\n",bai_name);
        exit(EXIT_FAILURE);
    }

    char magic[4];
    if((4 != fread(magic, 1, 4, fp))){
        assert(0);
    }

    static const char* BAI_MAGIC_STR = "BAI\1";
  
    if(strncmp(magic,BAI_MAGIC_STR,4) != 0){
        assert(0);
    }

    static const size_t i32s(sizeof(int32_t));
    static const size_t u32s(sizeof(uint32_t));
    static const size_t u64s(sizeof(uint64_t));

    int32_t n_ref(0);

    if(1 != fread(&n_ref,i32s,1,fp)){
        assert(0);
    }

    assert(n_ref >= 0);

    std::vector<bool> is_ref_present(n_ref,false);

    for(int32_t i(0);i<n_ref;++i){
        int32_t n_bin(0);
        if(1 != fread(&n_bin,i32s,1,fp)){
            assert(0);
        }

        assert(n_bin >= 0);
        is_ref_present[i] = (n_bin > 0);

        for(int32_t j(0);j<n_bin;++j){
            uint32_t bin(0);
            if(1 != fread(&bin,u32s,1,fp)){
                assert(0);
            }

            int32_t n_chunk(0);
            if(1 != fread(&n_chunk,i32s,1,fp)){
                assert(0);
            }
            assert(n_chunk >= 0);

            if(n_chunk>0) fseek(fp,n_chunk*u64s*2,SEEK_CUR);
        }

        int32_t n_intv(0);
        if(1 != fread(&n_intv,i32s,1,fp)){
            assert(0);
        }
        assert(n_intv >= 0);
            
        if(n_intv>0) fseek(fp,n_intv*u64s,SEEK_CUR);
    }
    fclose(fp);

    fprintf(stdout,"n_ref_ids: %i\n",n_ref);
    fprintf(stdout,"ref_ids_mapped in file: (zero-indexed)\n");
    for(int32_t i(0);i<n_ref;++i){
        if(is_ref_present[i]) fprintf(stdout,"%i\n",i);
    }
}