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Alignment: API rework. 'obi align' is now 'obi lcs', and the results are

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now written to columns automatically created in the output view, all
optimally handled at the C level.
This commit is contained in:
Celine Mercier
2016-12-12 11:58:59 +01:00
parent fa4e4ffaff
commit 8afb1644e9
11 changed files with 579 additions and 272 deletions
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4
src/sse_banded_LCS_alignment.h
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@ -21,7 +21,7 @@
// TODO doc
int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool lcsmode);
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode);
double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double threshold, bool normalize, int reference, bool similarity_mode);
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
#endif