dkopecek / libfasta Goto Github PK

I'm trying to compile your project here, but there is the most bizarre issue that I though I should message you before going down any rabbit holes. It appears that at compile time, fasta_read() returns type bool, despite the declaration in fasta.h being of type FASTA_rec_t*. Do you have an idea why this might be?

g++ -g -Wall -pipe -lfasta -lpthread --std=gnu++0x main.cpp -o mummer
main.cpp: In function ‘globalArgs parseArgs(int, char*)’:
main.cpp:229:25: error: cannot convert ‘bool’ to ‘FASTA_rec_t’ in assignment
while(tmpFastaRecord = fasta_read(inFile, NULL, 0, NULL) != NULL){

With the addition of more debugging resources and an improved bwt construction, I've tracked issues to the FASTA file opening, which actually takes up ~20 minutes and 8GB before segfaulting when loading human chromosome 2. I'm not sure where in the library this is yet, but that's the usage issue.

Need to start looking into the fasta_open() codepath.

Throughout the code, there is not a whole lot of documentation. For FASTA_req_t, seq could have new lines or not from a reading of the documentation, but this is easy to find for certain. What isn't is where the description strings are located. The header sections appear to hold indexing information and not any form of description strings. I can't be sure however, as the documentation is not complete enough.