void OpenMyBam(BamTools::BamReader &bamReader, char *bamFile){
if (!bamReader.Open(bamFile)) {
cerr << " ERROR: fail to open bam" << bamFile << endl;
//exit(-1); throw exception instead
}
//find the index
string bamIndex(bamFile);
// replace last character to find index
bamIndex.append(".bai"); // bam->bai
if (!bamReader.OpenIndex(bamIndex)) {
cerr << "ERROR: fail to open bam index " << bamIndex << endl;
// throw exception
}
}
void Config::InitializationClustering() {
struct stat st;
if(stat(Workspace.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Workspace directory already present");
else if (mkdir(Workspace.c_str(), 0755) != 0) {
Log("[Error] Could not create workspace directory: " + Workspace);
exit(1);
}
RunningTasksFile = Workspace + "/" + FilePrefix + "running.tasks";
StatsFile = Workspace + "/" + FilePrefix + "stats";
BinClusterFile = Workspace + "/" + FilePrefix + "bpc";
clusterFile = new ClusterFile(BinClusterFile);
clusterDir = Workspace + "/clusters/";
if(stat(clusterDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Cluster directory already present");
else if (mkdir(clusterDir.c_str(), 0755) != 0) {
Log("[Error] Could not create cluster directory: " + clusterDir);
exit(1);
}
insertsizeDir = Workspace + "/insertsize/";
if(stat(insertsizeDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Insertsize directory already present");
else if (mkdir(insertsizeDir.c_str(), 0755) != 0) {
Log("[Error] Could not create insertsize directory: " + insertsizeDir);
exit(1);
}
coverageDir = Workspace + "/coverage/";
if(stat(coverageDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Coverage directory already present");
else if (mkdir(coverageDir.c_str(), 0755) != 0) {
Log("[Error] Could not create coverage directory: " + coverageDir);
exit(1);
}
if (!ForwardBam.empty() && !ReverseBam.empty() && PairedBam.empty()) {
UsePairedBam = false;
} else if (ForwardBam.empty() && ReverseBam.empty() && !PairedBam.empty()) {
UsePairedBam = true;
} else {
Log("[Error] No correct bam file(s)");
exit(1);
}
BamTools::BamAlignment alignment;
BamTools::BamReader BamReader;
if (UsePairedBam) {
BamReader.Open(PairedBam);
if (not BamReader.IsOpen()) {
Log("[Error] Could not open paired bam");
exit(1);
}
if (PairedIndex.empty()) {
if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
PairedIndex = PairedBam.substr(0,PairedBam.find_last_of(".bam")-3) + ".bai";
BamReader.OpenIndex(PairedIndex);
}
if (not BamReader.HasIndex()) {
Log("[Error] No index for bamfile");
exit(1);
}
}
BamTools::SamHeader header = BamReader.GetHeader();
for (BamTools::SamReadGroupIterator it = header.ReadGroups.Begin(); it != header.ReadGroups.End(); it++) {
BamTools::SamReadGroup* readgroup = &*it;
readNameConverter.TrimName(readgroup->ID);
readNameConverter.AddReadGroup(readgroup->ID);
}
long int count = 0;
while (BamReader.GetNextAlignment(alignment)) {
string RG;
if (alignment.GetTag("RG", RG)) {
if (not NameTrim.empty()) readNameConverter.TrimName(RG);
if (readNameConverter.AddReadGroup(RG)) {
Log("[Warning] Readgroup '" + RG + "' found in reads but not in header");
count = 0;
}
}
count++;
if (count > 10000) break;
}
BamReader.Close();
} else {
BamReader.Open(ForwardBam);
if (not BamReader.IsOpen()) {
Log("[Error] Could not open first/forward bam");
exit(1);
}
if (ForwardIndex.empty()) {
if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
ForwardIndex = ForwardBam.substr(0,ForwardBam.find_last_of(".bam")-3) + ".bai";
BamReader.OpenIndex(ForwardIndex);
}
if (not BamReader.HasIndex()) {
Log("[Error] No index for forward bamfile");
exit(1);
}
}
BamTools::SamHeader forwardheader = BamReader.GetHeader();
for (BamTools::SamReadGroupIterator it = forwardheader.ReadGroups.Begin(); it != forwardheader.ReadGroups.End(); it++) {
BamTools::SamReadGroup* readgroup = &*it;
readNameConverter.TrimName(readgroup->ID);
readNameConverter.AddReadGroup(readgroup->ID);
}
long int count = 0;
while (BamReader.GetNextAlignment(alignment)) {
string RG;
if (alignment.GetTag("RG", RG)) {
if (!NameTrim.empty()) readNameConverter.TrimName(RG);
if (readNameConverter.AddReadGroup(RG)) {
Log("[Warning] Readgroup '" + RG + "' found in forward reads but not in header");
count = 0;
}
}
count++;
if (count > 10000) break;
}
BamReader.Close();
BamReader.Open(ReverseBam);
if (not BamReader.IsOpen()) {
Log("[Error] Could not open second/reverse bam");
exit(1);
}
if (ReverseIndex.empty()) {
if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
ReverseIndex = ReverseBam.substr(0,ReverseBam.find_last_of(".bam")-3) + ".bai";
BamReader.OpenIndex(ReverseIndex);
}
if (not BamReader.HasIndex()) {
Log("[Error] No index for reverse bamfile");
exit(1);
}
}
BamTools::SamHeader reverseheader = BamReader.GetHeader();
for (BamTools::SamReadGroupIterator it = reverseheader.ReadGroups.Begin(); it != reverseheader.ReadGroups.End(); it++) {
BamTools::SamReadGroup* readgroup = &*it;
readNameConverter.TrimName(readgroup->ID);
if (readNameConverter.AddReadGroup(readgroup->ID)) {
Log("[Warning] Readgroup '" + readgroup->ID + "' found in reverse but not in forward");
}
}
count = 0;
while (BamReader.GetNextAlignment(alignment)) {
string RG;
if (alignment.GetTag("RG", RG)) {
if (!NameTrim.empty()) readNameConverter.TrimName(RG);
if (readNameConverter.AddReadGroup(RG)) {
Log("[Warning] Readgroup '" + RG + "' found in reverse reads but not in header");
count = 0;
}
}
count++;
if (count > 10000) break;
}
BamReader.Close();
}
for(map<string, int>::iterator it = readNameConverter.ReadGroups.begin(); it!=readNameConverter.ReadGroups.end(); ++it) {
ostringstream logBuffer;
logBuffer << "Readgroup found: " << it->second << " - " << it->first;
Log(logBuffer.str());
}
writeConfigFile(Workspace + FilePrefix + "config");
}