IntronList.cpp

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#include <stdio.h>
#include <string.h>

#include <shogun/mathematics/Math.h>
#include <shogun/lib/config.h>
#include <shogun/io/SGIO.h>
#include <shogun/structure/IntronList.h>

using namespace shogun;

CIntronList::CIntronList()
:CSGObject()
{
    m_length = 0;
    m_all_pos = NULL;
    m_intron_list = NULL;
    m_quality_list = NULL;
}
CIntronList::~CIntronList()
{
    for (int i=0; i<m_length; i++)
    {
        SG_FREE(m_intron_list[i]);
        SG_FREE(m_quality_list[i]);
    }
    SG_FREE(m_intron_list);
    SG_FREE(m_quality_list);
    SG_FREE(m_all_pos);
}
void CIntronList::init_list(int32_t* all_pos, int32_t len)
{
    m_length = len;
    m_all_pos = SG_MALLOC(int32_t, len);
    memcpy(m_all_pos, all_pos, len*sizeof(int32_t));
    m_intron_list = SG_MALLOC(int32_t*, len);
    m_quality_list = SG_MALLOC(int32_t*, len);

    //initialize all elements with an array of length one
    int32_t* one;
    for (int i=0;i<m_length;i++)
    {
        one = SG_MALLOC(int32_t, 1);//use malloc here because mem can be increased efficiently with realloc later
        m_intron_list[i] = one;
        m_intron_list[i][0] = 1;
        one = SG_MALLOC(int32_t, 1);
        m_quality_list[i] = one;
        m_quality_list[i][0] = 1;
    }
}
void CIntronList::read_introns(int32_t* start_pos, int32_t* end_pos, int32_t* quality, int32_t len)
{
    int k=0;
    for(int i=0;i<m_length;i++)//iterate over candidate positions
    {
        while (k<len)
        {
            //SG_PRINT("i:%i, m_all_pos[i]:%i, k:%i, end_pos[k]: %i\n", i, m_all_pos[i], k, end_pos[k])
            if (k>0)
                if (end_pos[k]<end_pos[k-1])
                    SG_ERROR("end pos array is not sorted: end_pos[k-1]:%i end_pos[k]:%i\n", end_pos[k-1], end_pos[k])
            if (end_pos[k]>=m_all_pos[i])
                break;
            else
                k++;

        }
        while (k<len && end_pos[k]==m_all_pos[i])
        {
            //SG_PRINT("\tk:%i, end_pos[k]: %i, start_pos[k]:%i\n", k, end_pos[k], start_pos[k])
            ASSERT(start_pos[k]<end_pos[k])
            ASSERT(end_pos[k]<=m_all_pos[m_length-1])
            // intron list
            //------------
            int32_t from_list_len = m_intron_list[i][0];
            int32_t* new_list = SG_REALLOC(int32_t, m_intron_list[i], from_list_len, (from_list_len+1));
            if (new_list == NULL)
                SG_ERROR("IntronList: Out of mem 4")
            new_list[from_list_len]= start_pos[k];
            new_list[0]++;
            m_intron_list[i] = new_list;
            // quality list
            //--------------
            int32_t q_list_len = m_quality_list[i][0];
            //SG_PRINT("\t q_list_len:%i, from_list_len:%i \n",q_list_len, from_list_len)
            ASSERT(q_list_len==from_list_len)
            new_list = SG_REALLOC(int32_t, m_quality_list[i], q_list_len, (q_list_len+1));
            if (new_list == NULL)
                SG_ERROR("IntronList: Out of mem 5")
            new_list[q_list_len]= quality[k];
            new_list[0]++;
            m_quality_list[i] = new_list;

            k++;
        }
    }
}
void CIntronList::get_intron_support(int32_t* values, int32_t from_pos, int32_t to_pos)
{
    if (from_pos>=m_length)
        SG_ERROR("from_pos (%i) is not < m_length (%i)\n",to_pos, m_length)
    if (to_pos>=m_length)
        SG_ERROR("to_pos (%i) is not < m_length (%i)\n",to_pos, m_length)
    int32_t* from_list = m_intron_list[to_pos];
    int32_t* q_list = m_quality_list[to_pos];

    //SG_PRINT("from_list[0]: %i\n", from_list[0])

    int32_t coverage = 0;
    int32_t quality = 0;
    for (int i=1;i<from_list[0]; i++)
    {
        //SG_PRINT("from_list[%i]: %i, m_all_pos[from_pos]:%i\n", i,  from_list[i], m_all_pos[from_pos])
        if (from_list[i]==m_all_pos[from_pos])
        {
            //SG_PRINT("found intron: %i->%i\n", from_pos, to_pos )
            coverage = coverage+1;
            quality = CMath::max(quality, q_list[i]);
        }
    }
    values[0] = coverage;
    values[1] = quality;
}