giuliaguidi/xavier

XAVIER: High-Performance X-Drop Adaptive Banded Pairwise Alignment

xavier's Issues

Missing code?

The syntax on this line

if(? != VectorRegister::VECTORWIDTH)

is unfamiliar to me and also unfamiliar to both GCC 9.3.0 and clang 10.0.0.

It looks as though there's missing code here. This prevents XAVIER from compiling.

Extraneous lib

Consider dropping lib/libxavier.a from the codebase since it's a binary.

self-issue todo

If (read length < VECTORLENGTH).

omp

Hi!

The omp dependency in benchmark/utils.h is unnecessary ;)

• Armin

Cannot compile

Hell XAVIER team,

This has been mentioned but no fix (GCC 11):

src/trace.cpp:81:55: warning: missing initializer for member ‘xavier::Trace::AlignmentPair::decodedCigar’ [-Wmissing-field-initializers]
81 | AlignmentPair traceback = {"", 0, 0, 0};
| ^
src/trace.cpp:83:20: error: expected primary-expression before ‘?’ token
83 | if(? != VectorRegister::VECTORWIDTH)
| ^
src/trace.cpp:83:22: error: expected primary-expression before ‘!=’ token
83 | if(? != VectorRegister::VECTORWIDTH)
| ^~
src/trace.cpp:83:52: error: expected ‘:’ before ‘)’ token
83 | if(? != VectorRegister::VECTORWIDTH)
| ^
| :
src/trace.cpp:83:52: error: expected primary-expression before ‘)’ token
src/trace.cpp:154:17: error: jump to label ‘dp’
154 | dp:
| ^~
src/trace.cpp:84:30: note: from here
84 | goto dp;
| ^~
src/trace.cpp:93:24: note: crosses initialization of ‘size_t sq_diag_pos’
93 | size_t sq_diag_pos = 0;
| ^~~~~~~~~~~
src/trace.cpp:92:24: note: crosses initialization of ‘size_t sq_above_pos’
92 | size_t sq_above_pos = 0;
| ^~~~~~~~~~~~
src/trace.cpp:91:24: note: crosses initialization of ‘size_t sq_left_pos’
91 | size_t sq_left_pos = 0;
| ^~~~~~~~~~~
src/trace.cpp:88:24: note: crosses initialization of ‘size_t dp_pos’
88 | size_t dp_pos = itAtMax->antiDiag3.argmax();
| ^~~~~~
src/trace.cpp:87:22: note: crosses initialization of ‘std::reverse_iterator<__gnu_cxx::__normal_iterator<xavier::TraceEntry*, std::vectorxavier::TraceEntry > > itAtMax’
87 | auto itAtMax = trace.rbegin() + (trace.size() - 1 - maxPos);
| ^~~~~~~
make: *** [obj/trace.o] Error 1

Thanks,