CigarRoller.cpp

/*
 *  Copyright (C) 2010-2011  Regents of the University of Michigan
 *
 *   This program 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.
 *
 *   This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#include <stdio.h>
#include <stdlib.h>
#include "CigarRoller.h"

////////////////////////////////////////////////////////////////////////
//
// Cigar Roller Class
//


CigarRoller & CigarRoller::operator += (CigarRoller &rhs)
{
    std::vector<CigarOperator>::iterator i;
    for (i = rhs.cigarOperations.begin(); i != rhs.cigarOperations.end(); i++)
    {
        (*this) += *i;
    }
    return *this;
}


//
// Append a new operator at the end of the sequence.
//
CigarRoller & CigarRoller::operator += (const CigarOperator &rhs)
{
    // Adding to the cigar, so the query & reference indexes would be
    // incomplete, so just clear them.
    clearQueryAndReferenceIndexes();

    if (rhs.count==0)
    {
        // nothing to do
    }
    else if (cigarOperations.empty() || cigarOperations.back() != rhs)
    {
        cigarOperations.push_back(rhs);
    }
    else
    {
        // last stored operation is the same as the new one, so just add it in
        cigarOperations.back().count += rhs.count;
    }
    return *this;
}


CigarRoller & CigarRoller::operator = (CigarRoller &rhs)
{
    clear();

    (*this) += rhs;
    
    return *this;
}


//
void CigarRoller::Add(Operation operation, int count)
{
    CigarOperator rhs(operation, count);
    (*this) += rhs;
}


void CigarRoller::Add(char operation, int count)
{
    switch (operation)
    {
        case 0:
        case 'M':
            Add(match, count);
            break;
        case 1:
        case 'I':
            Add(insert, count);
            break;
        case 2:
        case 'D':
            Add(del, count);
            break;
        case 3:
        case 'N':
            Add(skip, count);
            break;
        case 4:
        case 'S':
            Add(softClip, count);
            break;
        case 5:
        case 'H':
            Add(hardClip, count);
            break;
        case 6:
        case 'P':
            Add(pad, count);
            break;
        default:
            // Hmmm... what to do?
            std::cerr << "ERROR "
                      << "(" << __FILE__ << ":" << __LINE__ <<"): "
                      << "Parsing CIGAR - invalid character found "
                      << "with parameter " << operation << " and " << count
                      << std::endl;
            break;
    }
}


void CigarRoller::Add(const char *cigarString)
{
    int operationCount = 0;
    while (*cigarString)
    {
        if (isdigit(*cigarString))
        {
            char *endPtr;
            operationCount = strtol((char *) cigarString, &endPtr, 10);
            cigarString = endPtr;
        }
        else
        {
            Add(*cigarString, operationCount);
            cigarString++;
        }
    }
}


bool CigarRoller::Remove(int index)
{
    if((index < 0) || ((unsigned int)index >= cigarOperations.size()))
    {
        // can't remove, out of range, return false.
        return(false);
    }
    cigarOperations.erase(cigarOperations.begin() + index);
    // Modifying the cigar, so the query & reference indexes are out of date,
    // so clear them.
    clearQueryAndReferenceIndexes();
    return(true);
}


bool CigarRoller::IncrementCount(int index, int increment)
{
    if((index < 0) || ((unsigned int)index >= cigarOperations.size()))
    {
        // can't update, out of range, return false.
        return(false);
    }
    cigarOperations[index].count += increment;

    // Modifying the cigar, so the query & reference indexes are out of date,
    // so clear them.
    clearQueryAndReferenceIndexes();
    return(true);
}


bool CigarRoller::Update(int index, Operation op, int count)
{
    if((index < 0) || ((unsigned int)index >= cigarOperations.size()))
    {
        // can't update, out of range, return false.
        return(false);
    }
    cigarOperations[index].operation = op;
    cigarOperations[index].count = count;

    // Modifying the cigar, so the query & reference indexes are out of date,
    // so clear them.
    clearQueryAndReferenceIndexes();
    return(true);
}


void CigarRoller::Set(const char *cigarString)
{
    clear();
    Add(cigarString);
}


void CigarRoller::Set(const uint32_t* cigarBuffer, uint16_t bufferLen)
{
    clear();

    // Parse the buffer.
    for (int i = 0; i < bufferLen; i++)
    {
        int opLen = cigarBuffer[i] >> 4;

        Add(cigarBuffer[i] & 0xF, opLen);
    }
}


//
// when we examine CIGAR strings, we need to know how
// many cumulative insert and delete positions there are
// so that we can adjust the read location appropriately.
//
// Here, we iterate over the vector of CIGAR operations,
// summaring the count for each insert or delete (insert
// increases the offset, delete decreases it).
//
// The use case for this is when we have a genome match
// position based on an index word other than the first one,
// and there is also a insert or delete between the beginning
// of the read and the index word.  We can't simply report
// the match position without taking into account the indels,
// otherwise we'll be off by N where N is the sum of this
// indel count.
//
// DEPRECATED - do not use.  There are better ways to accomplish that by using
// read lengths, reference lengths, span of the read, etc.
int CigarRoller::getMatchPositionOffset()
{
    int offset = 0;
    std::vector<CigarOperator>::iterator i;

    for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
    {
        switch (i->operation)
        {
            case insert:
                offset += i->count;
                break;
            case del:
                offset -= i->count;
                break;
                // TODO anything for case skip:????
            default:
                break;
        }
    }
    return offset;
}


//
// Get the string reprentation of the Cigar operations in this object.
// Caller must delete the returned value.
//
const char * CigarRoller::getString()
{
    // NB: the exact size of the string is not important, it just needs to be guaranteed
    // larger than the largest number of characters we could put into it.

    // we do not explicitly manage memory usage, and we expect when program exits, the memory used here will be freed
    static char *ret = NULL;
    static unsigned int retSize = 0;

    if (ret == NULL)
    {
        retSize = cigarOperations.size() * 12 + 1;  // 12 == a magic number -> > 1 + log base 10 of MAXINT
        ret = (char*) malloc(sizeof(char) * retSize);
        assert(ret != NULL);

    }
    else
    {
        // currently, ret pointer has enough memory to use
        if (retSize > cigarOperations.size() * 12 + 1)
        {
        }
        else
        {
            retSize = cigarOperations.size() * 12 + 1;
            free(ret);
            ret = (char*) malloc(sizeof(char) * retSize);
        }
        assert(ret != NULL);
    }

    char *ptr = ret;
    char buf[12];   // > 1 + log base 10 of MAXINT

    std::vector<CigarOperator>::iterator i;

    // Progressively append the character representations of the operations to
    // the cigar string we allocated above.

    *ptr = '\0';    // clear result string
    for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
    {
        sprintf(buf, "%d%c", (*i).count, (*i).getChar());
        strcat(ptr, buf);
        while (*ptr)
        {
            ptr++;    // limit the cost of strcat above
        }
    }
    return ret;
}


void CigarRoller::clear()
{
    // Clearing the cigar, so the query & reference indexes are out of
    // date, so clear them.
    clearQueryAndReferenceIndexes();
    cigarOperations.clear();
}