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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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Buffer overflow while creating index #19

Open tahuh opened 4 years ago

tahuh commented 4 years ago

Hi

I'm having trouble when creating index file.

Reference genome file was downloaded from Ensembl and added "chr" string to the reference name for chromosomes 1~22, X,Y,MT to use a certain tool that requires "chr" in reference name (other chromosomes starts with GL or others are unchanged).

After running index command bitmapperBS --index /path/to/genome.fa error message below has arose.

The length of Genome is 3101804739:
Open /synbiodata/reference/ensemble/GRCh37/Homo_sapiens.GRCh37.dna.primary_assembly.with.chr.fa.index.bs sucessfully! 
text_length=6203609478
*** buffer overflow detected ***: ./bitmapperBS terminated
Aborted (core dumped)

I have tried indexing using original reference genome and had no problem.

I'm attaching link to reference genome : ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/

Thomas.

chhylp123 commented 4 years ago

I will have a look at this bug. Thanks a lot.