https://github.com/isovic/graphmap
Tip revision: db1362c39748ba56374ac770a26adc0ae3ec054a authored by Ivan Sovic (T530) on 16 November 2015, 00:52:31 UTC
Fixed issues with overhanging bases when aligning near a gap while using anchored alignment. The first issue was that the incremental hash key should have been reset when an unknown base was met, because it couldn't be 2bitpacked. The other one was that SeqAn, unlike EDlib, reports alignments even if all bases are Xs. I placed a threshold on the edit distance on alignment of the front and back part of a read (before first and after last alignment). These parts should not have edit distance larger than half their length. Otherwise, the read will be clipped on that end.
Fixed issues with overhanging bases when aligning near a gap while using anchored alignment. The first issue was that the incremental hash key should have been reset when an unknown base was met, because it couldn't be 2bitpacked. The other one was that SeqAn, unlike EDlib, reports alignments even if all bases are Xs. I placed a threshold on the edit distance on alignment of the front and back part of a read (before first and after last alignment). These parts should not have edit distance larger than half their length. Otherwise, the read will be clipped on that end.
Tip revision: db1362c
| File | Mode | Size |
|---|---|---|
| doc | ||
| libs | ||
| reproducibility | ||
| scripts | ||
| src | ||
| .gitignore | -rw-r--r-- | 238 bytes |
| INSTALL | -rw-r--r-- | 586 bytes |
| LICENCE | -rw-r--r-- | 1.1 KB |
| Makefile | -rwxr-xr-x | 5.8 KB |
| README.md | -rw-r--r-- | 7.4 KB |
