forked from Yichen-Si/STAR
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Genome.cpp
executable file
·234 lines (200 loc) · 9.76 KB
/
Genome.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
#include "Genome.h"
#include "SuffixArrayFuns.h"
#include "PackedArray.h"
#include "ErrorWarning.h"
#include "streamFuns.h"
#include "SharedMemory.h"
#include "genomeScanFastaFiles.h"
#include "systemFunctions.h"
#include <time.h>
#include <cmath>
#include <unistd.h>
#include <sys/stat.h>
Genome::Genome (Parameters &P, ParametersGenome &pGe): shmStart(NULL), P(P), pGe(pGe), sharedMemory(NULL)
{
struct stat stbuf;
stat(pGe.gDir.c_str(), &stbuf);
shmKey=stbuf.st_ino;
genomeOut.g=this;//will change if genomeOut is different from genomeMain
genomeOut.convYes=false;
sjdbOverhang = pGe.sjdbOverhang; //will be re-defined later if another value was used for the generated genome
sjdbLength = pGe.sjdbOverhang==0 ? 0 : pGe.sjdbOverhang*2+1;
};
// Genome::~Genome()
// {
// if (sharedMemory != NULL)
// delete sharedMemory;
// sharedMemory = NULL;
// }
void Genome::freeMemory(){//free big chunks of memory used by genome and suffix array
if (pGe.gLoad=="NoSharedMemory") {//can deallocate only for non-shared memory
delete[] G1;
G1=NULL;
SA.deallocateArray();
SApass2.deallocateArray();
SAi.deallocateArray();
P.inOut->logMain << "RAM after freeing genome index memory:\n"
<< linuxProcMemory() << flush;
};
};
uint Genome::OpenStream(string name, ifstream & stream, uint size)
{
stream.open((pGe.gDir+ "/" +name).c_str(), ios::binary);
if (!stream.good()) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not open genome file: "<< pGe.gDir << "/" << name <<"\n";
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_GENOME_FILES, P);
};
if (size>0) {
P.inOut->logMain << name << ": size given as a parameter = " << size <<"\n";
} else {
P.inOut->logMain << "Checking " << name << " size";
stream.seekg (0, ios::end);
int64 size1 = stream.tellg();
if (size1<=0) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: failed reading from genome file: "<< pGe.gDir << "/" << name <<"\n";
errOut << "SOLUTION: re-generate the genome index\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, 1, P);
};
size=(uint) size1;
stream.clear();
stream.seekg (0, ios::beg);
P.inOut->logMain << "file size: "<< size <<" bytes; state: good=" <<stream.good()\
<<" eof="<<stream.eof()<<" fail="<<stream.fail()<<" bad="<<stream.bad()<<"\n"<<flush;
};
return size;
};
void Genome::HandleSharedMemoryException(const SharedMemoryException & exc, uint64 shmSize)
{
ostringstream errOut;
errOut << "Shared memory error: " << exc.GetErrorCode() << ", errno: " << strerror(exc.GetErrorDetail()) << "(" << errno << ")" << endl;
int exitCode = EXIT_CODE_SHM;
switch (exc.GetErrorCode())
{
case EOPENFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmget() or shm_open()." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case EEXISTS:
errOut << "EXITING: fatal error from shmget() trying to allocate shared memory piece." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl;
errOut << "Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v " << shmSize+2000000000 << endl;
errOut << "Possible cause 3: allowed shared memory size is not large enough. SOLUTIONS: (i) consult STAR manual on how to increase shared memory allocation; " \
"(ii) ask your system administrator to increase shared memory allocation; (iii) run STAR with --genomeLoad NoSharedMemory" << endl<<flush;
break;
case EFTRUNCATE:
errOut << "EXITING: fatal error from ftruncate() error shared memory." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl << flush;
exitCode = EXIT_CODE_MEMORY_ALLOCATION;
break;
case EMAPFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmat() while trying to get address of the shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case ECLOSE:
errOut << "EXITING because of FATAL ERROR: could not close the shared memory object." << endl << flush;
break;
case EUNLINK:
#ifdef POSIX_SHARED_MEM
errOut << "EXITING because of FATAL ERROR: could not delete the shared object." << endl << flush;
#else
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmctl() while trying to remove shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
#endif
break;
default:
errOut << "EXITING because of FATAL ERROR: There was an issue with the shared memory allocation. Try running STAR with --genomeLoad NoSharedMemory to avoid using shared memory.";
break;
}
try
{
if (sharedMemory != NULL)
sharedMemory->Clean();
}
catch(...)
{}
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, exitCode, P);
};
//////////////////////////////////////////////////////////////////////////////////////////
void Genome::chrInfoLoad() {//find chrStart,Length,nChr from Genome G
//load chr names
ifstream chrStreamIn ( (pGe.gDir+"/chrName.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrName.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
char chrInChar[1000];
while (chrStreamIn.good()) {
string chrIn;
chrStreamIn.getline(chrInChar,1000);
chrIn=chrInChar;
if (chrIn=="") break;
chrName.push_back(chrIn);
};
chrStreamIn.close();
nChrReal=chrName.size();
P.inOut->logMain << "Number of real (reference) chromosomes= " << nChrReal <<"\n"<<flush;
chrStart.resize(nChrReal+1);
chrLength.resize(nChrReal);
//load chr lengths
chrStreamIn.open( (pGe.gDir+"/chrLength.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrLength.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
for (uint ii=0;ii<nChrReal;ii++) {
chrStreamIn >> chrLength[ii];
};
chrStreamIn.close();
//load chr starts
chrStreamIn.open( (pGe.gDir+"/chrStart.txt").c_str() );
if (chrStreamIn.fail()) {
ostringstream errOut;
errOut << "EXITING because of FATAL error, could not open file " << (pGe.gDir+"/chrStart.txt") <<"\n";
errOut << "SOLUTION: re-generate genome files with STAR --runMode genomeGenerate\n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
for (uint ii=0;ii<=nChrReal;ii++) {
chrStreamIn >> chrStart[ii];
};
chrStreamIn.close();
//log
for (uint ii=0; ii<nChrReal;ii++) {
P.inOut->logMain << ii+1 <<"\t"<< chrName[ii] <<"\t"<<chrLength[ii]<<"\t"<<chrStart[ii]<<"\n"<<flush;
chrNameIndex[chrName[ii]]=ii;
};
//chr sets
for (auto &cm: pGe.chrSet.mitoStrings) {
uint64 ind1 = std::find(chrName.begin(), chrName.end(), cm) - chrName.begin();
pGe.chrSet.mito.insert(ind1);
};
};
//////////////////////////////////////////////////////////
void Genome::chrBinFill() {
chrBinN = chrStart[nChrReal]/genomeChrBinNbases+1;
chrBin = new uint [chrBinN];
for (uint ii=0, ichr=1; ii<chrBinN; ++ii) {
if (ii*genomeChrBinNbases>=chrStart[ichr]) ichr++;
chrBin[ii]=ichr-1;
};
};
//////////////////////////////////////////////////////////
void Genome::genomeSequenceAllocate(uint64 nGenomeIn, uint64 &nG1allocOut, char*& Gout, char*& G1out)
{
nG1allocOut=(nGenomeIn + 100)*2; //extra 100 bytes at the beginning, just in case
if (P.limitGenomeGenerateRAM < (nG1allocOut+nG1allocOut/3)) {//allocate nG1alloc/3 for SA generation
ostringstream errOut;
errOut <<"EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM="<< (P.limitGenomeGenerateRAM) <<"is too small for your genome\n";
errOut <<"SOLUTION: please specify --limitGenomeGenerateRAM not less than "<< nG1allocOut+nG1allocOut/3 <<" and make that much RAM available \n";
exitWithError(errOut.str(),std::cerr, P.inOut->logMain, EXIT_CODE_INPUT_FILES, P);
};
G1out=new char[nG1allocOut];
Gout=G1out+100;
memset(G1out,GENOME_spacingChar,nG1allocOut);//initialize to K-1 all bytes
};