seqan
seqan copied to clipboard
seqan
SeqAn's official repository.
I am trying to build an FM-Index over a 13GB fasta file. After one hour of processing with an average cpu-load of only 52% on one core the indexer used...
I get a compilation warning in include/seqan/sequence/sequence_lexical.h : 295. https://github.com/seqan/seqan/blob/584ae4fbff8312cfe31b3e0aea651edfb1b580ef/include/seqan/sequence/sequence_lexical.h#L295 I fixed the warning with: left_length = static_cast(right_length); Would that be the correct way of handling it? Thank you
using different cases is often done to express masking, it would be nice to have.
From Trac, @weese is this still an issue? In the case of paired reads where one mate aligns and the other does not, the SAM output of the FragmentStore is...
The FragmentStore does neither support soft nor hard clipping. For soft-clipping, the full sequence is in the SEQ field of SAM files and the anchor gaps data structure supports clipping...
The names of the functions hash2, hash2Next, hashUpper and hash2Upper are not clear enough to get the idea immediately. As far as I understand, the function hash2 forces the computation...
We need some means to align sequences against profiles. Here is some code: https://github.com/holtgrewe/align_profile
The following task would be a nice advanced tutorial: Input are two FASTQ files with reads that contain paired reads which length ~100bp, template size ~150-300bp. Many of the pairs...
When changing the underlying score type of a MatrixScore from standard `int` to `int16_t`, the SimdScoreWrapper issues a compile time error. Here the expected code: ```cpp Score mat{-1, -30}; ExecutionPolicy...
