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
|
#include "ParametersClip.h"
#include "Parameters.h"
#include "SequenceFuns.h"
#include "ErrorWarning.h"
void ParametersClip::initialize(Parameters *pPin)
{
pP = pPin;
//yes = false;
if (adapterType[0]!="Hamming" && adapterType[0]!="CellRanger4") {
exitWithError("EXITING because of fatal PARAMETER error: --clipAdapterType = " + adapterType[0] + " is not a valid option\n" +
"SOLUTION: use valid --adapterType options: Hamming OR CellRanger4\n", std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
for (uint32 im=0; im<in[0].adSeq.size(); im++) {//TODO implement standard 5p clipping
if (in[0].adSeq[im]!="-") {
exitWithError("EXITING because of fatal PARAMETER error: --clip5pAdapterSeq is not supported yet.\
\nSOLUTION: Do not use --clip5pAdapter* options.\n", std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
};
if (adapterType[0]=="CellRanger4") {
if (in[1].adSeq.size()>1 || in[1].adSeq[0]!="-") {
exitWithError("EXITING because of fatal PARAMETER error: --clipAdapterType CellRanger4 uses fixed sequences for 5' (TSO) and 3' (polyA) adapters."
"\nSOLUTION: Do not use --clip3pAdapter* or --clip5pAdapter* options.\n", std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
in[0].adSeq[0] = "AAGCAGTGGTATCAACGCAGAGTACATGGG";
in[1].adSeq[0] = "A";
};
for (int ip=0; ip<2; ip++) {//if no clipping, repeat for all mates
if (in[ip].adSeq[0]=="-") {
in[ip].adSeq.resize(pP->readNmates, "-");
in[ip].adMMp.resize(pP->readNmates, 0);
};
if (in[ip].N[0]==0)
in[ip].N.resize(pP->readNmates, 0);
if (in[ip].NafterAd[0]==0)
in[ip].NafterAd.resize(pP->readNmates, 0);
};
array<string,2> p53={"5","3"};
for (int ip=0; ip<2; ip++) {//check that readNmates values are provided
if (in[ip].adSeq.size() != pP->readNmates) {
exitWithError("EXITING because of fatal PARAMETER error: --clip" +p53[ip]+ "pAdapterSeq has to contain " +to_string(pP->readNmates)+ " values to match the number of mates."
"\nSOLUTION: specify " +to_string(pP->readNmates)+ "values in --clip" +p53[ip]+ "pAdapterSeq , for no clipping use -"
, std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
if (in[ip].adMMp.size() != pP->readNmates) {
exitWithError("EXITING because of fatal PARAMETER error: --clip" +p53[ip]+ "pAdapterMMp has to contain " +to_string(pP->readNmates)+ " values to match the number of mates."
"\nSOLUTION: specify " +to_string(pP->readNmates)+ "values in --clip" +p53[ip]+ "pAdapterMMp"
, std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
if (in[ip].NafterAd.size() != pP->readNmates) {
exitWithError("EXITING because of fatal PARAMETER error: --clip" +p53[ip]+ "pAfterAdapterNbases has to contain " +to_string(pP->readNmates)+ " values to match the number of mates."
"\nSOLUTION: specify " +to_string(pP->readNmates)+ "values in --clip" +p53[ip]+ "pAfterAdapterNbases , for no clipping use 0"
, std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
if (in[ip].N.size() != pP->readNmates) {
exitWithError("EXITING because of fatal PARAMETER error: --clip" +p53[ip]+ "pNbases has to contain " +to_string(pP->readNmates)+ " values to match the number of mates."
"\nSOLUTION: specify " +to_string(pP->readNmates)+ "values in --clip" +p53[ip]+ "pNbases , for no clipping use 0"
, std::cerr, pPin->inOut->logMain, EXIT_CODE_PARAMETER, *pPin);
};
};
};
void ParametersClip::initializeClipMates(vector<vector<ClipMate>> &clipMates)
{
clipMates.resize(pP->readNends);
for (uint32 im=0; im<clipMates.size(); im++) {
clipMates[im].resize(2);
for (int ip=0; ip<2; ip++) {//fill in the ip
clipMates[im][ip].type=ip;
if (adapterType[0]=="CellRanger4") {
clipMates[im][ip].type += 10;
};
if (im<pP->readNmates) {//true mates
clipMates[im][ip].initialize(in[ip].N[im], in[ip].adSeq[im], in[ip].NafterAd[im], in[ip].adMMp[im]);
} else {//barcode read, no clipping
//back() effectively duplicates the values for 2nd mate - if only one value was given in paramerter input
clipMates[im][ip].initialize(0, "-", 0, 0);
};
};
};
};
|
