When I compile with CXXFLAGS including -Wall and -Werror (these flags are enabled in abyss-dbgfm), the following code cannot be compiled:

fm_index.h:111: error: ‘outBase’ may be used uninitialized in this function

This isn't a time-sensitive issue as I can just compile without these flags.

Hi Jared,

Because BWTDiskReader maps the EOF symbol to a '$', count_map['$'] returns the number of strings plus one, and getNumStrings returns one more than expected. It's easy enough to fix, but I wanted to check that your work doesn't depend on this behaviour before I mucked with it.

https://github.com/jts/dbgfm/blob/master/bwtdisk_reader.cpp#L65
https://github.com/jts/dbgfm/blob/master/fm_index_builder.cpp#L81

Cheers,
Shaun

make produces the following error on OS X 10.8.4 with
i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

g++ -O3 -o dbgfm alphabet.cpp dbg_query.cpp fm_index_builder.cpp fm_index.cpp main.cpp sga_bwt_reader.cpp utility.cpp bwtdisk_reader.cpp
In file included from dbg_query.h:13,
                 from dbg_query.cpp:11:
fm_index.h: In member function ‘char FMIndex::getChar(size_t) const’:
fm_index.h:78: error: no matching function for call to ‘decode(const PackedTableDecoder&, const unsigned char*, const unsigned char*, size_t&, size_t&, StreamEncode::SingleBaseDecode&)’
fm_index.h: In member function ‘size_t FMIndex::getOcc(char, size_t) const’:
fm_index.h:121: error: no matching function for call to ‘decode(const PackedTableDecoder&, const unsigned char*, const unsigned char*, size_t&, size_t&, StreamEncode::BaseCountDecode&)’
…

I have encountered this failed assertion (assert(currBit / 8 < output.size());, stream_encoding.h:152) when loading a genome. It happens with the Drosophila melanogaster genome (FASTA download link). I have inspected the file and I can't find anything strange going on.

Does anyone have any ideas what would trigger this assertion to fail? Furthermore, any ideas for how I can fix it?

Thank you