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divonlan / genozip

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
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Buffer overflow on long reads. #13

Closed jkbonfield closed 3 years ago

jkbonfield commented 3 years ago

On a pacbio CLR long-read data set downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20131209_na12878_pacbio/si/NA12878.pacbio.bwa-sw.20140202.bam I get this error:

$ ~/lustre/genozip/genozip -@12 -f -e hs37d5.ref.genozip NA12878.pacbio.bwa-sw.20140202.bam
genozip NA12878.pacbio.bwa-sw.20140202.bam : 3% (39 minutes 29 seconds)*** buffer overflow detected ***: /nfs/users/nfs_j/jkb/lustre/genozip/genozip terminated
Aborted (core dumped)

This was built from the master branch, with git describe --tags claiming genozip-12.0.33-4-g308a84dd. The OS is Ubuntu 18.04.5 LTS (Bionic). I can't recall how I built it, but most likely it'd have just been "make" so using the system gcc with whatever optimisation options are listed in the Makefile.

divonlan commented 3 years ago

Hi James, thanks again for reporting this and thanks for your patience. This issue has now been fixed, and released in version 12.0.34.

jkbonfield commented 3 years ago

Thanks.