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
|
#include "SoloFeature.h"
#include "streamFuns.h"
SoloFeature::SoloFeature(Parameters &Pin, ReadAlignChunk **RAchunk, Transcriptome &inTrans, int32 feTy, SoloReadBarcode *readBarSumIn, SoloFeature **soloFeatAll)
: P(Pin), RAchunk(RAchunk), Trans(inTrans), featureType(feTy), soloFeatAll(soloFeatAll), pSolo(P.pSolo), readBarSum(readBarSumIn)
{
if (featureType>=0) {//otherwise we do not need these arrays - e.g. with --runMode soloCellFiltering
readFeatSum = new SoloReadFeature(featureType,P,-1);
readFeatAll = new SoloReadFeature*[P.runThreadN];
};
//number of features
switch (featureType) {
case SoloFeatureTypes::Gene :
case SoloFeatureTypes::GeneFull :
case SoloFeatureTypes::GeneFull_Ex50pAS :
case SoloFeatureTypes::GeneFull_ExonOverIntron :
case SoloFeatureTypes::Velocyto :
featuresNumber=Trans.nGe;
break;
case SoloFeatureTypes::SJ :
featuresNumber=P.sjAll[0].size();
break;
default:
featuresNumber = -1; //undefined
};
};
void SoloFeature::clearLarge()
{
cbFeatureUMImap.clear();
cbFeatureUMImap.shrink_to_fit();
countCellGeneUMI.clear();
countCellGeneUMI.shrink_to_fit();
countCellGeneUMIindex.clear();
countCellGeneUMIindex.shrink_to_fit();
countMatMult.i.clear();
countMatMult.i.shrink_to_fit();
countMatMult.m.clear();
countMatMult.m.shrink_to_fit();
//indCB.clear(); //needed for Velocyto
//indCB.shrink_to_fit();
indCBwl.clear();
indCBwl.shrink_to_fit();
nGenePerCB.clear();
nGenePerCB.shrink_to_fit();
nGenePerCBmulti.clear();
nGenePerCBmulti.shrink_to_fit();
nReadPerCB.clear();
nReadPerCB.shrink_to_fit();
nReadPerCBtotal.clear();
nReadPerCBtotal.shrink_to_fit();
nReadPerCBunique.clear();
nReadPerCBunique.shrink_to_fit();
nUMIperCB.clear();
nUMIperCB.shrink_to_fit();
nUMIperCBmulti.clear();
nUMIperCBmulti.shrink_to_fit();
nUMIperCBsorted.clear();
nUMIperCBsorted.shrink_to_fit();
sjAll[0].clear();
sjAll[0].shrink_to_fit();
sjAll[1].clear();
sjAll[1].shrink_to_fit();
};
|
