// -*- 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
///

#include "blt_util/bam_record.hh"



unsigned
bam_record::
alt_map_qual(const char* tag) const {
    uint8_t* alt_ptr(bam_aux_get(_bp,tag));
    if((NULL != alt_ptr) and is_int_code(alt_ptr[0])) {
        const int alt_map(bam_aux2i(alt_ptr));
        assert(alt_map>=0);
        return static_cast<unsigned>(alt_map);
    } else {
        return map_qual();
    }
}

const char* 
bam_record::
get_string_tag(const char* tag) const {

    // retrieve the BAM tag
    uint8_t* pTag = bam_aux_get(_bp, tag);
    if(!pTag) return NULL;

    // skip tags that are not encoded as a null-terminated string
    if(pTag[0] != 'Z') return NULL;
    ++pTag;

    return (const char*)pTag;
}

bool
bam_record::
get_num_tag(const char* tag, int32_t& num) const {

    // retrieve the BAM tag
    uint8_t* pTag = bam_aux_get(_bp, tag);
    if(!pTag) return false;

    // skip tags that are not encoded as integers
    if(!is_int_code(pTag[0])) return false;
    num = bam_aux2i(pTag);

    return true;
}