Luca Denti

Consensus coverage in diploid mode

8

Hi all, first of all: great library! I was playing around with diploid mode and I ran into strange segmentation faults (when freeing `cons_cov`). From what I could see, in...

It would a nice feature to allow user to define a temporary directory and use it when running samtools and salmon See #15

Hi, I noticed that the htsFile opened in the constructor is never closed. In very particular cases (like mine), this may cause crashes since there are too many open files...

Segmentation fault during geno step

1

Hi, when I try to run vargeno on the same data linked in my previous issue (https://github.com/medvedevgroup/vargeno/issues/2), it crashes during the geno step. This is the output of `vargeno index`:...

Output VCF file is empty

2

Hello, I tried to run vargeno (last commit, 00ee0f0affd626bfe7b1c04291e924341031240f) on the following data: [reference](http://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz), [VCFs](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) (provided by 1000genomes), and [sample](https://ftp-trace.ncbi.nlm.nih.g2ov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam) sequenced from NA12878 individual. I ran some tests on different...

Pull request related to Issue https://github.com/medvedevgroup/vargeno/issues/2

Hi, I am trying to include unannotated splice-sites in the index but whippet keeps crashing. I prepared the bam file as suggested on the README (I aligned the reads with...