[med-svn] [mothur] 01/04: Imported Upstream version 1.37.6
Tomasz Buchert
tomasz at moszumanska.debian.org
Wed Jun 22 20:59:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
tomasz pushed a commit to branch master
in repository mothur.
commit 30c91fee4483beb138f43659c15dcab40ffc4cf2
Author: Tomasz Buchert <tomasz at debian.org>
Date: Wed Jun 22 22:15:33 2016 +0200
Imported Upstream version 1.37.6
---
Makefile | 13 +-
Mothur.xcodeproj/project.pbxproj | 8 +-
source/commands/makecontigscommand.cpp | 79 ++++------
source/commands/makecontigscommand.h | 269 +++++++++------------------------
4 files changed, 105 insertions(+), 264 deletions(-)
diff --git a/Makefile b/Makefile
index 5cfd853..bc86111 100755
--- a/Makefile
+++ b/Makefile
@@ -13,9 +13,10 @@ OPTIMIZE ?= yes
USEREADLINE ?= yes
USEBOOST ?= yes
BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"4/18/2016\""
-VERSION = "\"1.37.1\""
+RELEASE_DATE = "\"6/20/2016\""
+VERSION = "\"1.37.6\""
ifeq ($(strip $(64BIT_VERSION)),yes)
CXXFLAGS += -DBIT_VERSION
@@ -44,14 +45,10 @@ ifeq ($(strip $(USEREADLINE)),yes)
endif
-#The boost libraries allow you to read gz files.
+#User specified boost library
ifeq ($(strip $(USEBOOST)),yes)
-#User specified boost library path
-ifeq ($(strip $(BOOST_LIBRARY_DIR)),"\"Enter_your_boost_library_path_here\"")
-else
- LDFLAGS += ${BOOST_LIBRARY_DIR}
-endif
+ LDFLAGS += -L ${BOOST_LIBRARY_DIR}
LIBS += -lboost_iostreams -lz
CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index a89af44..7bf0eb8 100755
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -3465,8 +3465,8 @@
GCC_MODEL_TUNING = "";
GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.36.0\\\"\"",
- "RELEASE_DATE=\"\\\"07/23/2015\\\"\"",
+ "VERSION=\"\\\"1.37.6\\\"\"",
+ "RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_VERSION = "";
@@ -3565,8 +3565,8 @@
ENABLE_STRICT_OBJC_MSGSEND = YES;
GCC_C_LANGUAGE_STANDARD = "compiler-default";
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.0\\\"\"",
- "RELEASE_DATE=\"\\\"04/05/2015\\\"\"",
+ "VERSION=\"\\\"1.37.6\\\"\"",
+ "RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
);
GCC_WARN_64_TO_32_BIT_CONVERSION = NO;
GCC_WARN_ABOUT_RETURN_TYPE = YES_ERROR;
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
index fb34c16..3a8b62d 100644
--- a/source/commands/makecontigscommand.cpp
+++ b/source/commands/makecontigscommand.cpp
@@ -953,6 +953,9 @@ unsigned long long MakeContigsCommand::createProcessesGroups(vector< vector<stri
//divide files between processors
int remainingPairs = fileInputs.size();
+
+ if (remainingPairs < processors) { processors = remainingPairs; }
+
int startIndex = 0;
for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
int numPairs = remainingPairs; //case for last processor
@@ -1170,7 +1173,7 @@ unsigned long long MakeContigsCommand::createProcessesGroups(vector< vector<stri
for(int h=1; h<processors; h++ ){
string extension = toString(h) + ".temp"; processIDS.push_back(h);
- contigsData* tempcontig = new contigsData(format, delim, group, align, outputDir, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, oligosfile, reorient, pdiffs, bdiffs, tdiffs, kmerSize, createOligosGroup, createFileGroup, allFiles, trimOverlap, h, fileInputs, startEndIndexes[h].start, startEndIndexes[h].end, compositeGroupFile+extension, compositeFastaFile+extension, compositeScrapFastaFile+extension, compositeQualFile+extension, compositeScrapQualFile+extension, comp [...]
+ contigsData* tempcontig = new contigsData(format, delim, group, align, outputDir, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, oligosfile, reorient, pdiffs, bdiffs, tdiffs, kmerSize, createOligosGroup, createFileGroup, allFiles, trimOverlap, h, fileInputs, startEndIndexes[h].start, startEndIndexes[h].end, compositeGroupFile+extension, compositeFastaFile+extension, compositeScrapFastaFile+extension, compositeQualFile+extension, compositeScrapQualFile+extension, comp [...]
pDataArray.push_back(tempcontig);
hThreadArray[h-1] = CreateThread(NULL, 0, MyGroupContigsThreadFunction, pDataArray[h-1], 0, &dwThreadIdArray[h-1]);
@@ -1691,7 +1694,7 @@ unsigned long long MakeContigsCommand::createProcesses(vector<string> fileInputs
}
int spot = (h)*2;
- contigsData* tempcontig = new contigsData(format, delim, group, fileInputs, qualOrIndexFiles, (outputFasta + extension), (outputScrapFasta + extension), (outputQual + extension), (outputScrapQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, tempFASTAFileNames, tempQUALFileNames, oligosfile, reorient, pdiffs, bdiffs, tdiffs, kmerSize, createOligosGroup, createFileGroup, allFiles, trimOverlap, lines[spot].start, lines[spot] [...]
+ contigsData* tempcontig = new contigsData(format, delim, group, fileInputs, qualOrIndexFiles, (outputFasta + extension), (outputScrapFasta + extension), (outputQual + extension), (outputScrapQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, tempFASTAFileNames, tempQUALFileNames, oligosfile, reorient, pdiffs, bdiffs, tdiffs, kmerSize, createOligosGroup, createFileGroup, allFiles, trimOverlap, lines[spot].start, lines[spot] [...]
pDataArray.push_back(tempcontig);
hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
@@ -2508,9 +2511,6 @@ int MakeContigsCommand::setNameType(string forward, string reverse) {
string tempReverse = reverse;
if (pos2 != string::npos) { tempReverse = reverse.substr(0, pos2); }
- if (pos2 == pos) { poundMatchPos = pos; }
- else { poundMatchPos = 0; }
-
if (tempForward == tempReverse) { type = poundMatch; }
}
@@ -2550,7 +2550,7 @@ int MakeContigsCommand::setNameType(string forwardFile, string reverseFile, char
}else { //compressed files
#ifdef USE_BOOST
m->openInputFileBinary(forwardFile, inForward, inFF);
- m->openInputFileBinary(reverseFile, inForward, inRF);
+ m->openInputFileBinary(reverseFile, inReverse, inRF);
if (delim == '>') {
Sequence fread(inFF);
@@ -3292,13 +3292,8 @@ bool MakeContigsCommand::fixName(string& forward){
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward = (forward.substr(0, poundMatchPos));
- }else { //it does not match
- int pos = forward.find_last_of('#');
- if (pos != string::npos) { forward = forward.substr(0, pos); }
- }
+ int pos = forward.find_last_of('#');
+ if (pos != string::npos) { forward = forward.substr(0, pos); }
}else if (nameType == perfectMatch) { match = true; }
return match;
@@ -3319,27 +3314,23 @@ bool MakeContigsCommand::checkName(FastqRead& forward, FastqRead& reverse){
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward.setName(forward.getName().substr(0, poundMatchPos));
- reverse.setName(reverse.getName().substr(0, poundMatchPos));
- }else { //it does not match
- string forwardName = forward.getName();
- string reverseName = reverse.getName();
-
- int pos = forwardName.find_last_of('#');
- if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
-
- int pos2 = reverseName.find_last_of('#');
- if (pos2 != string::npos) { reverseName = reverseName.substr(0, pos2); }
-
- if (forwardName == reverseName) {
- forward.setName(forwardName);
- reverse.setName(reverseName);
- }else{
- match = false;
- }
+
+ string forwardName = forward.getName();
+ string reverseName = reverse.getName();
+
+ int pos = forwardName.find_last_of('#');
+ if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
+
+ int pos2 = reverseName.find_last_of('#');
+ if (pos2 != string::npos) { reverseName = reverseName.substr(0, pos2); }
+
+ if (forwardName == reverseName) {
+ forward.setName(forwardName);
+ reverse.setName(reverseName);
+ }else{
+ match = false;
}
+
}else if (nameType == perfectMatch) { match = true; }
return match;
@@ -3359,11 +3350,6 @@ bool MakeContigsCommand::checkName(Sequence& forward, Sequence& reverse){
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward.setName(forward.getName().substr(0, poundMatchPos));
- reverse.setName(reverse.getName().substr(0, poundMatchPos));
- }else { //it does not match
string forwardName = forward.getName();
string reverseName = reverse.getName();
@@ -3379,7 +3365,6 @@ bool MakeContigsCommand::checkName(Sequence& forward, Sequence& reverse){
}else{
match = false;
}
- }
}else if (nameType == perfectMatch) { match = true; }
return match;
@@ -3399,11 +3384,7 @@ bool MakeContigsCommand::checkName(QualityScores& forward, QualityScores& revers
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward.setName(forward.getName().substr(0, poundMatchPos));
- reverse.setName(reverse.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = forward.getName();
string reverseName = reverse.getName();
@@ -3419,7 +3400,7 @@ bool MakeContigsCommand::checkName(QualityScores& forward, QualityScores& revers
}else{
match = false;
}
- }
+
}else if (nameType == perfectMatch) { match = true; }
return match;
@@ -3441,11 +3422,7 @@ bool MakeContigsCommand::checkName(Sequence& forward, QualityScores& reverse){
if (nameType == poundMatch) {
match = true;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- forward.setName(forward.getName().substr(0, poundMatchPos));
- reverse.setName(reverse.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = forward.getName();
string reverseName = reverse.getName();
@@ -3461,7 +3438,7 @@ bool MakeContigsCommand::checkName(Sequence& forward, QualityScores& reverse){
}else{
match = false;
}
- }
+
}else if (nameType == perfectMatch) { match = true; }
return match;
diff --git a/source/commands/makecontigscommand.h b/source/commands/makecontigscommand.h
index 3c36fd4..146d25b 100644
--- a/source/commands/makecontigscommand.h
+++ b/source/commands/makecontigscommand.h
@@ -68,7 +68,7 @@ private:
string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, findexfile, rindexfile, file, format, inputDir;
string outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, outputGroupFileName, group;
float match, misMatch, gapOpen, gapExtend;
- int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq, kmerSize, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, poundMatchPos, nameType;
+ int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq, kmerSize, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, nameType;
vector<string> outputNames;
Oligos* oligos;
@@ -121,7 +121,7 @@ struct contigsData {
vector<vector<string> > fastaFileNames, qualFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
- int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq, kmerSize, poundMatchPosition, nameType;
+ int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq, kmerSize, nameType;
bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap, reorient, gz, renameSeqs;
map<string, int> groupCounts;
map<string, string> groupMap;
@@ -134,7 +134,7 @@ struct contigsData {
contigsData(){}
- contigsData(string form, char d, string g, vector<string> f, vector<string> qif, string of, string osf, string oq, string osq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, vector<vector<string> > ffn, vector<vector<string> > qfn,string olig, bool ro, int pdf, int bdf, int tdf, int km, bool cg, bool cfg, bool all, bool to, unsigned long long lff, unsigned long long lff2, unsigned long long lrf, unsigned long long lrf2, unsigned [...]
+ contigsData(string form, char d, string g, vector<string> f, vector<string> qif, string of, string osf, string oq, string osq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, vector<vector<string> > ffn, vector<vector<string> > qfn,string olig, bool ro, int pdf, int bdf, int tdf, int km, bool cg, bool cfg, bool all, bool to, unsigned long long lff, unsigned long long lff2, unsigned long long lrf, unsigned long long lrf2, unsigned [...]
inputFiles = f;
qualOrIndexFiles = qif;
outputFasta = of;
@@ -173,10 +173,9 @@ struct contigsData {
format = form;
done=false;
renameSeqs = false;
- poundMatchPosition = pmp;
nameType = nt;
}
- contigsData(string form, char d, string g, string al, string opd, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, string olig, bool ro, int pdf, int bdf, int tdf, int km, bool cg, bool cfg, bool all, bool to, int tid, vector< vector<string> > fileI, int st, int ed, string compGroupFile, string compFastaFile, string compScrapFastaFile, string compQualFile, string compScrapQualFile, string compMisMatchFile, map<string, int> tGroupCounts, map<int, stri [...]
+ contigsData(string form, char d, string g, string al, string opd, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, int delt, string olig, bool ro, int pdf, int bdf, int tdf, int km, bool cg, bool cfg, bool all, bool to, int tid, vector< vector<string> > fileI, int st, int ed, string compGroupFile, string compFastaFile, string compScrapFastaFile, string compQualFile, string compScrapQualFile, string compMisMatchFile, map<string, int> tGroupCounts, map<int, stri [...]
m = mout;
match = ma;
misMatch = misMa;
@@ -215,7 +214,6 @@ struct contigsData {
file2Group = fGroup;
gz = gzb;
renameSeqs = ren;
- poundMatchPosition = pmp;
nameType = nt;
}
};
@@ -234,7 +232,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
try {
unsigned long long numReads = 0;
pDataArray->delim = '@';
- int poundMatchPos = pDataArray->poundMatchPosition;
string format = pDataArray->format;
for (int l = pDataArray->start; l < pDataArray->end; l++) {
@@ -279,9 +276,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
string tempReverse = reverse;
if (pos2 != string::npos) { tempReverse = reverse.substr(0, pos2); }
- if (pos2 == pos) { poundMatchPos = pos; }
- else { poundMatchPos = 0; }
-
if (tempForward == tempReverse) { type = poundMatch; }
}
@@ -545,7 +539,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
qual_score[0] = -2; qual_score[1] = -1.58147; qual_score[2] = -0.996843; qual_score[3] = -0.695524; qual_score[4] = -0.507676; qual_score[5] = -0.38013; qual_score[6] = -0.289268; qual_score[7] = -0.222552; qual_score[8] = -0.172557; qual_score[9] = -0.134552; qual_score[10] = -0.105361; qual_score[11] = -0.0827653; qual_score[12] = -0.0651742; qual_score[13] = -0.0514183; qual_score[14] = -0.0406248; qual_score[15] = -0.0321336; qual_score[16] = -0.0254397; qual_score[17] = [...]
int longestBase = 1000;
- int poundMatchPos = pDataArray->poundMatchPosition;
Alignment* alignment;
if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
@@ -672,11 +665,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -692,7 +681,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -703,10 +692,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -722,7 +708,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
FastqRead r2read(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
@@ -732,10 +718,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -751,7 +734,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -778,10 +761,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- firead.setName(firead.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = firead.getName();
@@ -797,7 +777,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -807,10 +787,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- f2iread.setName(f2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = f2iread.getName();
@@ -826,7 +803,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -844,10 +821,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- riread.setName(riread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = riread.getName();
@@ -863,7 +837,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -873,10 +847,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2iread.setName(r2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2iread.getName();
@@ -892,7 +863,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -910,10 +881,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -929,7 +897,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -941,10 +909,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -960,7 +925,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
@@ -971,10 +936,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -990,7 +952,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
@@ -1013,11 +975,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -1033,7 +991,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -1060,11 +1018,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -1080,7 +1034,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -1091,11 +1045,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -1111,7 +1061,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
@@ -1121,11 +1071,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -1141,7 +1087,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
@@ -1168,11 +1114,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- firead.setName(firead.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = firead.getName();
@@ -1188,7 +1130,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -1196,11 +1138,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- f2iread.setName(f2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
string forwardName = fread.getName();
string reverseName = f2iread.getName();
@@ -1216,7 +1153,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -1233,11 +1170,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- riread.setName(riread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = riread.getName();
@@ -1253,7 +1186,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -1261,11 +1194,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2iread.setName(r2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2iread.getName();
@@ -1281,7 +1210,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -1299,11 +1228,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -1319,7 +1244,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -1329,11 +1254,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -1349,7 +1270,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
@@ -1359,11 +1280,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -1379,7 +1296,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; }
@@ -1402,11 +1319,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -1422,7 +1335,7 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -2182,7 +2095,6 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
*/
int longestBase = 1000;
- int poundMatchPos = pDataArray->poundMatchPosition;
Alignment* alignment;
if(pDataArray->align == "gotoh") { alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase); }
@@ -2297,11 +2209,6 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
//////////////////////////////////////////////////////////////
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -2317,7 +2224,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -2327,11 +2234,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -2347,7 +2250,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
FastqRead r2read(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
@@ -2356,11 +2259,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -2376,7 +2275,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
@@ -2403,11 +2302,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- firead.setName(firead.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = firead.getName();
@@ -2423,7 +2318,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -2433,11 +2328,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
/////////////////////////////////////////////////////////////
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- f2iread.setName(f2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = f2iread.getName();
@@ -2453,7 +2344,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -2471,11 +2362,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- riread.setName(riread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = riread.getName();
@@ -2491,7 +2378,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
@@ -2502,11 +2389,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2iread.setName(r2iread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2iread.getName();
@@ -2522,7 +2405,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -2540,11 +2423,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -2560,7 +2439,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
@@ -2570,11 +2449,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- f2read.setName(f2read.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = f2read.getName();
string reverseName = rread.getName();
@@ -2590,7 +2465,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) {
@@ -2600,11 +2475,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- r2read.setName(r2read.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = r2read.getName();
@@ -2620,7 +2491,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
@@ -2643,11 +2514,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- if (poundMatchPos) {
- fread.setName(fread.getName().substr(0, poundMatchPos));
- rread.setName(rread.getName().substr(0, poundMatchPos));
- }else { //it does not match
+
string forwardName = fread.getName();
string reverseName = rread.getName();
@@ -2663,7 +2530,7 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else{
fixed = false;
}
- }
+
}else if (pDataArray->nameType == perfectMatch) { fixed = true; }
/////////////////////////////////////////////////////////////
if (!fixed) {
--
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