/**
 ** Copyright (c) 2007-2010 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).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 **/

#include <cstring>
#include "smallRna/TrimmerResult.h"

char CTrimmerResult::ms_PrefixString[MAX_READ_SIZE];

void CTrimmerResult::Print(char * readString,
                           int    threshold,
                           char * preString)
{
    if (m_Status != OKAY)
    {
        printf(">ERROR STATUS=%d\n", m_Status);
        if (preString) printf("%s\t", preString);
        printf("%s\n", readString);
    }
    else
    {
        memcpy(ms_PrefixString, readString, m_SuffixPosition);
        ms_PrefixString[m_SuffixPosition] = 0;
        printf(">%s-%s:%d:%d:%s\n", ms_PrefixString, readString + m_SuffixPosition, m_Count, m_Score, m_Matcher);

        if (preString) printf("%s\t", preString);
        if (m_Score > threshold) printf("%s\n", ms_PrefixString);
        else printf("%s\n", readString);
    }
}

void CTrimmerResult::PrintFastq(char * readString,
				int    threshold,
				char * name1,
				char * name2,
				char * qualityString,
				int    nPadLen,
				int    nExtraBases,
				TrimmerReport & report )
{

  if (m_Status != OKAY) {
      printf(">ERROR STATUS=%d\n", m_Status);
      printf("%s\t", name1);
      printf("%s\n", readString);
  } else {
    // Three possibilities:
    // 0.) nPadLen == -1 means do not pad with Ns, just trim
    // 1.) m_suffixPosition <= nPadLen
    //     then, add (nPadLen - m_suffixPosition) N's to readString
    // 2.) m_suffixPosition > nPadLen
    //     then, m_suffixPosition == nPadLen

    int readLength = strlen( readString );
    int cutPosition;

    if ( m_Score > threshold ) {
      cutPosition = m_SuffixPosition;
      if ( cutPosition >= 1 ) {
	cutPosition -= nExtraBases;
      }
    }
    else {
      cutPosition = readLength;
    }
    if (cutPosition > nPadLen && nPadLen != -1 ) {
      cutPosition = nPadLen;
    }
    if (report.Flag()) {
      report.Add( cutPosition, readLength );
    }

    memcpy(ms_PrefixString, readString, cutPosition);
    char prefixQualityString[MAX_READ_SIZE];
    memcpy(prefixQualityString, qualityString, cutPosition);
    ms_PrefixString[cutPosition]     = 0;
    prefixQualityString[cutPosition] = 0;

    // Pad out with N's if required
    if ( nPadLen != -1  ) {  // -1 value for nPadLen means do not pad, just trim.
      for (int ii = cutPosition; ii < nPadLen; ii++) {
	ms_PrefixString[ii]     = 'N';
	prefixQualityString[ii] = 'h';
      }
      ms_PrefixString[nPadLen]     = 0;
      prefixQualityString[nPadLen] = 0;
    }

    // Print Fastq record
    printf("%s\n", name1);
    printf("%s\n", ms_PrefixString);
    printf("%s\n", name2);
    printf("%s\n", prefixQualityString);

  }
}


void CTrimmerResult::Print(FILE * & fpWrite,
                           char *   readString,
                           int      threshold,
                           char *   preString)
{
    if (m_Status != OKAY)
    {
        fprintf(fpWrite, ">ERROR STATUS=%d\n", m_Status);
        if (preString) fprintf(fpWrite, "%s\t", preString);
        fprintf(fpWrite, "%s\n", readString);
    }
    else
    {
        memcpy(ms_PrefixString, readString, m_SuffixPosition);
        ms_PrefixString[m_SuffixPosition] = 0;
        fprintf(fpWrite, ">%s-%s:%d:%d:%s\n", ms_PrefixString, readString + m_SuffixPosition, m_Count, m_Score, m_Matcher);

        if (preString) fprintf(fpWrite, "%s\t", preString);
        if (m_Score > threshold) fprintf(fpWrite, "%s\n", ms_PrefixString);
        else fprintf(fpWrite, "%s\n", readString);
    }
}