diff options
| author | Andreas Tille <tille@debian.org> | 2017-01-09 12:53:15 +0100 |
|---|---|---|
| committer | Andreas Tille <tille@debian.org> | 2017-01-09 12:53:15 +0100 |
| commit | 7b7c16b4fb27697c91f6a582084e35d35b71799f (patch) | |
| tree | 02e786898de30ff307df505f0646a1eb12fec6f4 /aligner_seed2.cpp | |
| parent | cce9c2f9961d60ca0e6a4ec949c380541d28f1ef (diff) | |
New upstream version 2.3.0
Diffstat (limited to 'aligner_seed2.cpp')
| -rw-r--r-- | aligner_seed2.cpp | 19 |
1 files changed, 9 insertions, 10 deletions
diff --git a/aligner_seed2.cpp b/aligner_seed2.cpp index 2bf75a8..0a9d90a 100644 --- a/aligner_seed2.cpp +++ b/aligner_seed2.cpp @@ -1825,11 +1825,10 @@ int main(int argc, char **argv) { // GCTATATAGCGCGCTTGCATCATTTTGTGT // ^ bool packed = false; - int color = 0; pair<Ebwt*, Ebwt*> ebwts = Ebwt::fromStrings<SString<char> >( strs, packed, - color, + 0, REF_READ_REVERSE, Ebwt::default_bigEndian, Ebwt::default_lineRate, @@ -1846,8 +1845,8 @@ int main(int argc, char **argv) { false, // autoMem false); // sanity - ebwts.first->loadIntoMemory (color, -1, true, true, true, true, false); - ebwts.second->loadIntoMemory(color, 1, true, true, true, true, false); + ebwts.first->loadIntoMemory (0, -1, true, true, true, true, false); + ebwts.second->loadIntoMemory(0, 1, true, true, true, true, false); int testnum = 0; @@ -2036,7 +2035,7 @@ int main(int argc, char **argv) { ebwts = Ebwt::fromStrings<SString<char> >( strs, packed, - color, + 0, REF_READ_REVERSE, Ebwt::default_bigEndian, Ebwt::default_lineRate, @@ -2053,8 +2052,8 @@ int main(int argc, char **argv) { false, // autoMem false); // sanity - ebwts.first->loadIntoMemory (color, -1, true, true, true, true, false); - ebwts.second->loadIntoMemory(color, 1, true, true, true, true, false); + ebwts.first->loadIntoMemory (0, -1, true, true, true, true, false); + ebwts.second->loadIntoMemory(0, 1, true, true, true, true, false); // Test to see if the root selector works as we expect { @@ -2985,7 +2984,7 @@ int main(int argc, char **argv) { ebwts = Ebwt::fromStrings<SString<char> >( strs, packed, - color, + 0, REF_READ_REVERSE, Ebwt::default_bigEndian, Ebwt::default_lineRate, @@ -3002,8 +3001,8 @@ int main(int argc, char **argv) { false, // autoMem false); // sanity - ebwts.first->loadIntoMemory (color, -1, true, true, true, true, false); - ebwts.second->loadIntoMemory(color, 1, true, true, true, true, false); + ebwts.first->loadIntoMemory (0, -1, true, true, true, true, false); + ebwts.second->loadIntoMemory(0, 1, true, true, true, true, false); // Query is longer than ftab and matches exactly once with one read gap, // one ref gap, and one mismatch |