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//==============================================================
// Name : PerM
// Author : Yangho Chen at University of southern California.
// Version : 0.4.0
// Copyright : Open source
// Description : C++, Ansi-style
//============================================================================
#include "PairedReadsMapping.h"
#include "ReadsMapping.h"
#include "Genome_Index_TableQ.h"
#include "PairedReadsSet.h"
#include "ReadInBitsSet.h"
#include "ReadInBits.h"
#include "ParameterList.h"
#include "Filename.h"
#include "chdir.h"
#include "stdafx.h"
#include <string>
#include <vector>
#include <iostream>
using namespace std;
time_t startt, endt;
bool retriveReadSetsAndSettings\
(ParameterList& P, vector<string>& readSetsList1, vector<string>& readSetsList2)
{
// (1) check reference
if (!P.checkRefValidity()) {
return(false);
}
// (2) check reads files
if (getReadSetsFilenames(P, readSetsList1, readSetsList2)) {
if ((int)readSetsList1.size() > 0) {
const char* firstReadSetFileName = readSetsList1.at(0).c_str();
P.bMappedSOLiDRead = P.bMappedSOLiDRead ||\
is_colorspace_reads(P.readsFileFormat) ||\
is_colorspace_reads(firstReadSetFileName);
P.cFileFormatSymbol = getReadsFileFormatSymbol(firstReadSetFileName, P.readsFileFormat);
P.readLength = getReadLength(firstReadSetFileName, P.cFileFormatSymbol);
} else {
LOG_INFO("Info %d: Cannot get read set from the read list.\n", ERROR_LOG);
return(false);
}
} else if (atoi(P.readsFile) >= (int)MIN_READ_LENGTH) {
P.bMakeIndex = true;
P.bSaveIndex = true;
P.bMappedSOLiDRead = is_colorspace_reads(P.readsFileFormat);
P.readLength = atoi(P.readsFile); // Must call P.truncatReadLength() later.
} else if (atoi(P.readsFile) > 0) {
LOG_INFO("Info %d: Incorrect reads file or the read length is too short\n", ERROR_LOG);
return(false);
} else {
return(false); // can not open the read file
}
P.truncatReadLength(); // truncated reads according to options or mapping long reads
// (3) select seed according to the setting
P.seedId = selectSeed(P);
// (4) avoid to use the same name
if (readSetsList1.size() > 1)
P.outputFileN[0] = '\0';
// (5) TODO remove the mask repeat process
P.bMaskedMathRepeat \
= (!P.bMatePairedReads && !P.bMappedLongRead && P.bExcludeAmbiguousReads);
bool validSetting = true;
validSetting &= printOptWarning4PairedEndOpts(P);
validSetting &= printOptWarning4PairedEndOpts(P);
return(validSetting);
}
string get_Index_Path(ParameterList P)
{
if (hasTheExtName(P.refFile, ".index") || P.refFormat == "index" ) {
return(string(P.refFile));
} else {
string indexPath = default_index_path(getBasename\
(P.refFile), P.bMappedSOLiDRead, P.seedId, P.readLength);
return(indexPath);
}
}
void setQueryIndexSubThreshold(CGenome_Index_TableQ& indexTable, unsigned int subDiffThreshold)
{
const unsigned int MAX_SUB_WHEN_QUERY_TABLE = 20;
if (subDiffThreshold > MAX_SUB_WHEN_QUERY_TABLE) {
indexTable.uiSubDiffThreshold = MAX_SUB_WHEN_QUERY_TABLE;
} else {
indexTable.uiSubDiffThreshold = subDiffThreshold;
}
}
bool buildIndexTable(CGenome_Index_TableQ& indexTable, ParameterList& P)
{
if (P.refFormat == "index" || hasTheExtName(P.refFile, ".index")) {
LOG_INFO("\nInfo %d: Index file %s has incorrect format\n", ERROR_LOG, P.refFile);
} else if (indexTable.getSeqFromFasta(P.refFile, P.refFormat)) {
bool bMaskedMathRepeat = P.bMaskedMathRepeat && (atoi(P.readsFile) != 0);
bool bMakeIndexSucessful = indexTable.make_index_table(P.anchorLength, P.seedId, P.bMappedSOLiDRead, bMaskedMathRepeat);
if (bMakeIndexSucessful) {
if (P.bSaveIndex) {
const bool bPrintErrMsg = true;
indexTable.save_index_table(P.indexFileN, bPrintErrMsg);
}
indexTable.bExcludeAmbiguous = P.bExcludeAmbiguousReads;
setQueryIndexSubThreshold(indexTable, P.subDiffThreshold);
return(true);
} else {
LOG_INFO("\nInfo %d: Faile to build index file %s.\n", ERROR_LOG, P.indexFileN);
}
}
return(false);
}
/*
* The main function construct or read in the index of a set of reference genome.
* It maps the reads
*/
int main(int argc, const char* argv[])
{
// testLongBases2Colors();
// (1) Get parameters.
ParameterList P = getParameterList(argc, argv);
if (argc <= 2) return 0;
vector<string> readSetsList1, readSetsList2;
bool validSetting = retriveReadSetsAndSettings(P, readSetsList1, readSetsList2);
if (validSetting) {
P.printSetting();
} else {
LOG_INFO("\nInfo %d: Invalid or confusing command. Check the opt\n", CONFIG_LOG);
#ifdef WIN32
STRIKE_KEY2CONTINUE;
#endif
return(-1);
}
// (2) Build or read index table
CGenome_Index_TableQ indexTable;
indexTable.uiSubDiffThreshold = (unsigned int)P.subDiffThreshold;
string indexPath = get_Index_Path(P);
const bool bPrintWarning = false;
if (P.bMakeIndex || indexTable.read_index_table(indexPath.c_str(), bPrintWarning) == false) {
if (buildIndexTable(indexTable, P) == false ) {
return(-1);
}
}
// testGenome_Index_TableQ(&indexTable);
// testMappingLongRead(&indexTable);
// (3) Mapped reads.
if ( P.bMatePairedReads && !P.bMappedLongRead ) {
if (readSetsList1.size() > 0 && (readSetsList1.size() == readSetsList2.size())) {
TIME_INFO(parallelMappingPairedReads\
(readSetsList1, readSetsList2, indexTable, P),"Mapping paired reads\n");
} else {
TIME_INFO(parallelMappingPairedReads\
(readSetsList1, indexTable, P), "Mapping paired reads");
}
} else if (P.bMatePairedReads && P.bMappedLongRead ) {
TIME_INFO(parallelMappingPairedLongReads(readSetsList1, readSetsList2, indexTable, P),\
"Mapped paired-ended long reads");
} else if ( !P.bMatePairedReads && P.bMappedLongRead ) {
TIME_INFO(parallelMappingLongReads(readSetsList1, indexTable, P),\
"Mapped single-ended long reads");
} else if ( !P.bMatePairedReads && !P.bMappedLongRead ) {
TIME_INFO(parallelMapping(readSetsList1, indexTable, P),\
"Mapped single-ended reads");
}
cout << endl;
return 0;
}
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