C++ Genome::fillInContigLengths方法代码示例

//.........这里部分代码省略.........
    for (unsigned i = 0; i < chromosomePaddingSize; i++) {
        paddingBuffer[i] = 'n';
    }
    paddingBuffer[chromosomePaddingSize] = '\0';

    bool warningIssued = false;
    bool inAContig = false;

    while (NULL != reallocatingFgets(&lineBuffer, &lineBufferSize, fastaFile)) {
        if (lineBuffer[0] == '>') {
            inAContig = true;
            //
            // A new contig.  Add in the padding first.
            //
            genome->addData(paddingBuffer);

            //
            // Now supply the chromosome name.
            //
            if (NULL != pieceNameTerminatorCharacters) {
                for (int i = 0; i < strlen(pieceNameTerminatorCharacters); i++) {
                    char *terminator = strchr(lineBuffer+1, pieceNameTerminatorCharacters[i]);
                    if (NULL != terminator) {
                        *terminator = '\0';
                    }
                }
            }
            if (spaceIsAPieceNameTerminator) {
                char *terminator = strchr(lineBuffer, ' ');
                if (NULL != terminator) {
                    *terminator = '\0';
                }
                terminator = strchr(lineBuffer, '\t');
                if (NULL != terminator) {
                    *terminator = '\0';
                }
            }
            char *terminator = strchr(lineBuffer, '\n');
            if (NULL != terminator) {
                *terminator = '\0';
            }
            terminator = strchr(lineBuffer, '\r');
            if (NULL != terminator) {
                *terminator = '\0';
            }
            genome->startContig(lineBuffer+1);
        } else {
            if (!inAContig) {
                WriteErrorMessage("\nFASTA file doesn't beging with a contig name (i.e., the first line doesn't start with '>').\n");
                soft_exit(1);
            }

            //
            // Convert it to upper case and truncate the newline before adding it to the genome.
            //

            char *newline = strchr(lineBuffer, '\n');
            if (NULL != newline) {
                *newline = 0;
            }

            //
            // But convert any 'N' to 'n'.  This is so we don't match the N from the genome with N
            // in reads (where we just do a straight text comparison.
            //
            size_t lineLen = strlen(lineBuffer);

			for (unsigned i = 0; i < lineLen; i++) {
              lineBuffer[i] = toupper(lineBuffer[i]);
            }

			for (unsigned i = 0; i < lineLen; i++) {
                if ('N' == lineBuffer[i]) {
                    lineBuffer[i] = 'n';
                }

                if (!isValidGenomeCharacter[(unsigned char)lineBuffer[i]]) {
                    if (!warningIssued) {
                        WriteErrorMessage("\nFASTA file contained a character that's not a valid base (or N): '%c', full line '%s'; \nconverting to 'N'.  This may happen again, but there will be no more warnings.\n", lineBuffer[i], lineBuffer);
                        warningIssued = true;
                    }
                    lineBuffer[i] = 'N';
                }
            }
            genome->addData(lineBuffer);
        }
    }

    //
    // And finally add padding at the end of the genome.
    //
    genome->addData(paddingBuffer);
    genome->fillInContigLengths();
    genome->sortContigsByName();

    fclose(fastaFile);
    delete [] paddingBuffer;
    delete [] lineBuffer;
    return genome;
}

//.........这里部分代码省略.........
    if (!openFileAndGetSizes(fileName,&loadFile,&nBases,&nContigs)) {
        //
        // It already printed an error.  Just fail.
        //
        return NULL;
    }

    if (0 == length) {
        length = nBases - i_minOffset;
    } else {
        //
        // Don't let length go beyond nBases.
        //
        length = __min(length,nBases - i_minOffset);
    }

    Genome *genome = new Genome(nBases,length, chromosomePadding);
   
    genome->nBases = nBases;
    genome->nContigs = genome->maxContigs = nContigs;
    genome->contigs = new Contig[nContigs];
    genome->minOffset = i_minOffset;
    if (i_minOffset >= nBases) {
        WriteErrorMessage("Genome::loadFromFile: specified minOffset %u >= nBases %u\n",i_minOffset,nBases);
    }

 

    genome->maxOffset = i_minOffset + length;

    static const unsigned contigNameBufferSize = 512;
    char contigNameBuffer[contigNameBufferSize];
    unsigned n;
    size_t contigSize;
    char *curName;
    for (unsigned i = 0; i < nContigs; i++) {
        if (NULL == loadFile->gets(contigNameBuffer, contigNameBufferSize)){
	  
	  WriteErrorMessage("Unable to read contig description\n");
            delete genome;
            return NULL;
        }

	for (n = 0; n < contigNameBufferSize; n++){
	  if (contigNameBuffer[n] == ' ') {
	    contigNameBuffer[n] = '\0'; 
	    break;
	  }
	}

    genome->contigs[i].beginningOffset = atoi(contigNameBuffer);
	contigNameBuffer[n] = ' '; 
	n++; // increment n so we start copying at the position after the space
	contigSize = strlen(contigNameBuffer + n) - 1; //don't include the final \n
    genome->contigs[i].name = new char[contigSize + 1];
    genome->contigs[i].nameLength = (unsigned)contigSize;
	curName = genome->contigs[i].name;
	for (unsigned pos = 0; pos < contigSize; pos++) {
	  curName[pos] = contigNameBuffer[pos + n];
	}
        curName[contigSize] = '\0';
    }

    //
    // Skip over the miserable \n that gets left in the file.
    //
    /*  char newline;
    if (1 != fread(&newline,1,1,loadFile)) {
        WriteErrorMessage("Genome::loadFromFile: Unable to read expected newline\n");
        delete genome;
        return NULL;
    }

    if (newline != 10) {
        WriteErrorMessage("Genome::loadFromFile: Expected newline to be 0x0a, got 0x%02x\n",newline);
        delete genome;
        return NULL;
    }
    */

    if (0 != loadFile->advance(i_minOffset)) {
        WriteErrorMessage("Genome::loadFromFile: _fseek64bit failed\n");
        soft_exit(1);
    }

    size_t retval;
    if (length != (retval = loadFile->read(genome->bases,length))) {
        WriteErrorMessage("Genome::loadFromFile: fread of bases failed; wanted %u, got %d\n", length, retval);
        loadFile->close();
        delete loadFile;
        delete genome;
        return NULL;
    }

    loadFile->close();
    delete loadFile;
    genome->fillInContigLengths();
    genome->sortContigsByName();
    return genome;
}

//.........这里部分代码省略.........
    if (!openFileAndGetSizes(fileName, &loadFile, &nBases, &nContigs, map)) {
        //
        // It already printed an error.  Just fail.
        //
        return NULL;
    }

    GenomeLocation maxLocation(nBases);

    if (0 == length) {
        length = maxLocation - minLocation;
    } else {
        //
        // Don't let length go beyond nBases.
        //
        length = __min(length, maxLocation - minLocation);
        maxLocation = minLocation + length;
    }

    Genome *genome = new Genome(nBases, length, chromosomePadding);
   
    genome->nBases = nBases;
    genome->nContigs = genome->maxContigs = nContigs;
    genome->contigs = new Contig[nContigs];
    genome->minLocation = minLocation;
    if (GenomeLocationAsInt64(minLocation) >= nBases) {
        WriteErrorMessage("Genome::loadFromFile: specified minOffset %u >= nBases %u\n", GenomeLocationAsInt64(minLocation), nBases);
        soft_exit(-1);
    }

    genome->maxLocation = maxLocation;

    static const unsigned contigNameBufferSize = 512;
    char contigNameBuffer[contigNameBufferSize];
    unsigned n;
    size_t contigSize;
    char *curName;
    for (unsigned i = 0; i < nContigs; i++) {
        if (NULL == loadFile->gets(contigNameBuffer, contigNameBufferSize)){
	  
	  WriteErrorMessage("Unable to read contig description\n");
            delete genome;
            return NULL;
        }

	for (n = 0; n < contigNameBufferSize; n++){
	  if (contigNameBuffer[n] == ' ') {
	    contigNameBuffer[n] = '\0'; 
	    break;
	  }
	}

    _int64 contigStart;
    if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) {
        WriteErrorMessage("Unable to parse contig start in genome file '%s', '%s%'\n", fileName, contigNameBuffer);
        soft_exit(1);
    }
    genome->contigs[i].beginningLocation = GenomeLocation(contigStart);
	contigNameBuffer[n] = ' '; 
	n++; // increment n so we start copying at the position after the space
	contigSize = strlen(contigNameBuffer + n) - 1; //don't include the final \n
    genome->contigs[i].name = new char[contigSize + 1];
    genome->contigs[i].nameLength = (unsigned)contigSize;
	curName = genome->contigs[i].name;
	for (unsigned pos = 0; pos < contigSize; pos++) {
	  curName[pos] = contigNameBuffer[pos + n];
	}
        curName[contigSize] = '\0';
    }

    if (0 != loadFile->advance(GenomeLocationAsInt64(minLocation))) {
        WriteErrorMessage("Genome::loadFromFile: _fseek64bit failed\n");
        soft_exit(1);
    }

    size_t readSize;
	if (map) {
		GenericFile_map *mappedFile = (GenericFile_map *)loadFile;
		genome->bases = (char *)mappedFile->mapAndAdvance(length, &readSize);
		genome->mappedFile = mappedFile;
		mappedFile->prefetch();
	} else {
		readSize = loadFile->read(genome->bases, length);

		loadFile->close();
		delete loadFile;
		loadFile = NULL;
	}

	if (length != readSize) {
		WriteErrorMessage("Genome::loadFromFile: fread of bases failed; wanted %u, got %d\n", length, readSize);
		delete loadFile;
		delete genome;
		return NULL;
	}
	
	genome->fillInContigLengths();
    genome->sortContigsByName();
    return genome;
}