/usr/include/pbseq/alignment/files/ReaderAgglomerateImpl.hpp is in libblasr-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #ifndef _BLASR_READER_AGGLOMERATE_IMPL_HPP_
#define _BLASR_READER_AGGLOMERATE_IMPL_HPP_
template<typename T_Sequence>
int ReaderAgglomerate::GetNext(T_Sequence & seq, int & randNum) {
randNum = rand();
return GetNext(seq);
}
template<typename T_Sequence>
int ReadChunkByNReads(ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxNReads) {
T_Sequence seq;
int nReads = 0;
while(nReads < maxNReads) {
if (reader.GetNext(seq)) {
reads.push_back(seq);
++nReads;
}
else {
break;
}
}
return nReads;
}
template<typename T_Sequence>
int ReadChunkBySize (ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxMemorySize) {
T_Sequence seq;
int nReads = 0;
int totalStorage = 0;
while (totalStorage < maxMemorySize) {
if (reader.GetNext(seq)) {
reads.push_back(seq);
totalStorage += seq.GetStorageSize();
nReads++;
}
else {
break;
}
}
return nReads;
}
#endif
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