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
235
236
237
238
239
240
241
|
#include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "serviceFuns.cpp"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
#include "SoloFeatureTypes.h"
#include<unistd.h> // for get_current_dir
void SoloFeature::outputResults(bool cellFilterYes, string outputPrefixMat)
{
//make directories
createDirectory(outputPrefixMat,P.runDirPerm, "Solo output directory", P);
/* old way, does not work when parent directores are needed
if (mkdir(outputPrefixMat.c_str(),P.runDirPerm)!=0 && errno!=EEXIST) {//create directory
exitWithError("EXITING because of fatal OUTPUT FILE error: could not create Solo output directory" + outputPrefixMat +
"\nSOLUTION: check the path and permisssions\n",
std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
};
*/
/////////////////////////////////////////////////////////////
//write features.tsv
switch (featureType) {
case SoloFeatureTypes::Gene :
case SoloFeatureTypes::GeneFull :
case SoloFeatureTypes::GeneFull_Ex50pAS :
case SoloFeatureTypes::GeneFull_ExonOverIntron :
case SoloFeatureTypes::Velocyto :
case SoloFeatureTypes::VelocytoSimple :
{
ofstream &geneStr=ofstrOpen(outputPrefixMat+pSolo.outFileNames[1],ERROR_OUT, P);
for (uint32 ii=0; ii<Trans.nGe; ii++) {
geneStr << Trans.geID[ii] <<"\t"<< (Trans.geName[ii].empty() ? Trans.geID[ii] : Trans.geName[ii]);
if (pSolo.outFormat.featuresGeneField3!="-") {
geneStr <<'\t'<< pSolo.outFormat.featuresGeneField3;
};
geneStr << '\n';
};
geneStr.close();
break;
};
case SoloFeatureTypes::SJ :
string sjout; //full path to SJ.out.tab with user-defined prefix
if (P.outFileNamePrefix[0]=='/') {
sjout = P.outFileNamePrefix + "SJ.out.tab";
} else {
char cwd [4096];
getcwd(cwd,4096);
sjout.append(cwd);
sjout += '/' + P.outFileNamePrefix + "SJ.out.tab";
};
remove((outputPrefixMat+pSolo.outFileNames[1]).c_str()); //remove symlink before creating it
if ( symlink(sjout.c_str(), (outputPrefixMat+pSolo.outFileNames[1]).c_str()) != 0 )
exitWithError("EXITING because of fatal OUTPUT FILE error: could not sym-link "
+ sjout + " into " + outputPrefixMat+pSolo.outFileNames[1]
+ "\nSOLUTION: check the path and permisssions\n",
std::cerr, P.inOut->logMain, EXIT_CODE_PARAMETER, P);
};
////////////////////////////////////////////////////////////////////////////
//write barcodes.tsv
ofstream &cbStr=ofstrOpen(outputPrefixMat+pSolo.outFileNames[2],ERROR_OUT, P);
uint64 nCellGeneEntries=0;//total number of non-zero cell/gene combinations (entries in the output matrix)
if (cellFilterYes) {//filtered cells
for (uint32 icb=0; icb<nCB; icb++) {
if (filteredCells.filtVecBool[icb]) {
cbStr << pSolo.cbWLstr[indCB[icb]] <<'\n';
nCellGeneEntries += nGenePerCB[icb];
};
};
} else {//unfiltered cells
for (uint64 ii=0; ii<pSolo.cbWLsize; ii++) {
cbStr << pSolo.cbWLstr[ii] <<'\n';
};
for (uint32 icb=0; icb<nCB; icb++) {
nCellGeneEntries += nGenePerCB[icb];
};
};
cbStr.flush();
/////////////////////////////////////////////////////////////
//output counting matrix
for (uint32 iCol=1; iCol<countMatStride; iCol++) {
string matrixFileName=outputPrefixMat;
if (featureType == SoloFeatureTypes::Velocyto) {
const array<string,3> velonames = {"spliced.mtx", "unspliced.mtx", "ambiguous.mtx"};
matrixFileName += velonames[iCol-1];
} else if (iCol>1 && cellFilterYes) {
break; //if cellFilterYes, only output first iCol, since filtering is only done for it
} else if (pSolo.umiDedup.types.size()>1) {
matrixFileName += "umiDedup-" + pSolo.umiDedup.typeNames[pSolo.umiDedup.types[iCol-1]] + ".mtx";
} else {
matrixFileName += pSolo.outFileNames[3];
};
ofstream &countMatrixStream=ofstrOpen(matrixFileName,ERROR_OUT, P);
//header
countMatrixStream <<"%%MatrixMarket matrix coordinate integer general\n";
countMatrixStream <<"%\n";
countMatrixStream << featuresNumber <<' '<< (cellFilterYes ? filteredCells.nCells : pSolo.cbWLsize) <<' '<< nCellGeneEntries << '\n';
uint32 cbInd1=0;
for (uint32 icb=0; icb<nCB; icb++) {
if (cellFilterYes) {
if (filteredCells.filtVecBool[icb]) {
++cbInd1;
} else {
continue;
};
} else {
cbInd1=indCB[icb]+1;
};
for (uint32 ig=0; ig<nGenePerCB[icb]; ig++) {
uint32 indG1=countCellGeneUMIindex[icb]+ig*countMatStride;
//feature index, CB index, count
countMatrixStream << countCellGeneUMI[indG1]+1 <<' '<< cbInd1 <<' '<< countCellGeneUMI[indG1+iCol] << '\n';
};
};
countMatrixStream.close();
};
//////////////////////////////////////////// output unique+multimappers
if (pSolo.multiMap.yes.multi && !cellFilterYes
&& (featureType == SoloFeatureTypes::Gene || featureType == SoloFeatureTypes::GeneFull
|| featureType == SoloFeatureTypes::GeneFull_ExonOverIntron || featureType == SoloFeatureTypes::GeneFull_Ex50pAS) ) {
//skipping unique
nUMIperCBmulti.resize(nCB);
nGenePerCBmulti.resize(nCB);
bool nGeneUMIperCBmultiFill = true; //if true, need to fill the arrays
for (const auto &iMult: pSolo.multiMap.types) {
for (uint32 iDed=0; iDed<pSolo.umiDedup.yes.N; iDed++) {
string matrixFileName=outputPrefixMat + "UniqueAndMult-" + pSolo.multiMap.typeNames[iMult];
if (pSolo.umiDedup.types.size()>1) {
matrixFileName += "_umiDedup-" + pSolo.umiDedup.typeNames[pSolo.umiDedup.types[iDed]];
};
matrixFileName += ".mtx";
uint32 mIndex = pSolo.multiMap.countInd.I[iMult] + iDed;
//string matOutString;
//matOutString.reserve(100000000);
std::ostringstream matOutStringStream;//(matOutString);
nCellGeneEntries = 0;
uint32 cbInd1=0;
for (uint32 icb=0; icb<nCB; icb++) {
cbInd1=indCB[icb]+1;
/* just unique
for (uint32 igm=countCellGeneUMIindex[icb]; igm<countCellGeneUMIindex[icb+1]; igm+=countMatStride) {
//feature index, CB index, count
matOutString += to_string(countCellGeneUMI[igm]+1) +' '+ to_string(cbInd1) +' '+ to_string(countCellGeneUMI[igm+iDed]) + '\n';
++nCellGeneEntries;
};
*/
/*//just multiple
for (uint32 igm=countMatMult.i[icb]; igm<countMatMult.i[icb+1]; igm+=countMatMult.s) {
matOutStringStream << int(countMatMult.m[igm])+1 <<' '<< cbInd1 <<' '<< countMatMult.m[igm+mIndex] <<'\n';
++nCellGeneEntries;
};
*/
//if (false)
{//sum unique+multiple: go over sorted lists. TODO: use a map to combine (check efficiency)
auto igm1 = countCellGeneUMIindex[icb];
auto igm2 = countMatMult.i[icb];
while ( igm1<countCellGeneUMIindex[icb+1] || igm2<countMatMult.i[icb+1] ) {
uint32 g1,c1=0,g2;
double c2=0;
if (igm1<countCellGeneUMIindex[icb+1]) {
g1 = countCellGeneUMI[igm1];
c1 = countCellGeneUMI[igm1+1+iDed];
} else {
g1 = (uint32)-1;
};
if (igm2<countMatMult.i[icb+1]) {
g2 = countMatMult.m[igm2];
c2 = countMatMult.m[igm2+mIndex];
} else {
g2 = (uint32)-1;
};
if (g1<g2) {//only unique counts for this gene
matOutStringStream << g1+1 <<' '<< cbInd1 <<' '<< c1 <<'\n';
igm1 += countMatStride;
} else if (g1>g2) {//only multiple counts for this gene
matOutStringStream << g2+1 <<' '<< cbInd1 <<' '<< c2 <<'\n';
igm2 += countMatMult.s;
if (nGeneUMIperCBmultiFill) {
nUMIperCBmulti[icb] += c2;
nGenePerCBmulti[icb]++;
};
} else {//unique and multiple counts for this gene
matOutStringStream << g1+1 <<' '<< cbInd1 <<' '<< c1+c2 <<'\n';
igm1 += countMatStride;
igm2 += countMatMult.s;
if (nGeneUMIperCBmultiFill) {
nUMIperCBmulti[icb] += c2;
};
};
++nCellGeneEntries;
};
};
};
//matOutStringStream.flush();
nGeneUMIperCBmultiFill = false; //arrays were filled - only do it once
ofstream &countMatrixStream=ofstrOpen(matrixFileName, ERROR_OUT, P);
//header
countMatrixStream <<"%%MatrixMarket matrix coordinate real general\n";
countMatrixStream <<"%\n";
countMatrixStream << featuresNumber <<' '<< pSolo.cbWLsize <<' '<< nCellGeneEntries << '\n';
countMatrixStream << matOutStringStream.str();
countMatrixStream.close();
};
};
};
};
|
