https://github.com/edawson/kseq_reader
A threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng Li
https://github.com/edawson/kseq_reader
Last synced: 4 months ago
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A threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng Li
- Host: GitHub
- URL: https://github.com/edawson/kseq_reader
- Owner: edawson
- Created: 2018-02-12T11:18:41.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-03-27T13:50:45.000Z (about 7 years ago)
- Last Synced: 2025-01-07T20:47:08.522Z (5 months ago)
- Language: C++
- Homepage:
- Size: 161 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# kseq_reader
A threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng Li
## Compiling
````
git clone --recursive https://github.com/edawson/kseq_reader
make
## To use in your code, compile with -lksr (and make
## sure the library is in your LD_LIBRARY_PATH and the
## header in LD_INCLUDE_PATH
````
## Usage
```
#include "kseq_reader.hpp"
using namespace std;
using namespace KSR; // Need to access kseq_reader items through namespace 'KSR'
int main(){
// You can construct a file, then open it
KSEQ_Reader kr;
kr.open("reads.fq");
// Or use the overloaded constructor and pass your filename
KSEQ_Reader kt("reads.fq");
// You can change the number of reads read in at a time but only
// BEFORE reading from the file.
kr.buffer_size(1000);
// Get the next 1000 reads
ksequence_t seq;
int num = 0;
int ret = kr.get_next_buf(seq, num);
// seq now contains a pointer to num ksequence_t's,
// which are structs with the following members:
//char* name;
//int name_len;
// char* quality;
// int qual_len;
// char* comment;
// int comment_len;
// char* sequence;
// uint32_t length;
// You can iterate over an entire file (max(buffer size, number of reads left)) like so:
int l = 0;
while(l == 0){
kt.get_next_buf(seq, num);
for (int i = 0; i < num; i++){
cout << seq.name << endl;
}
}
// get_next_buf will return non-zero if the file can't be read or there are no more lines,
// and the loop will terminate.
// You can also just get one ksequence_t at a time:
kr.next(seq);
}
```