Pierre Lindenbaum

Hi, thank you for the bug report, I'm away from my code for now but my guess is that this bug is produced when some chromosomes are just too small...

which program are you running ? what was the command line ?

I don't think there is a problem: some of your sequences have a very large deletion. ``` >4:98103819 ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------agctttgaagagagcagtggttc tcccaggacgcagctggagatctgagaacggg----cagactgcctcctcaagtgggtcc...

the program scans from 5' to 3' and , for the deletions, search for the '-'. For one deletion and as long as you're going to have some '-' at...

an idea: '-' are interpreted as a deletion. try to replace the leading and trailing '-' with spaces.

have a look at `V.getAttribute*` in https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/variant/variantcontext/VariantContext.html

I've just fixed a problem with the 'tests' but the gradle issue above is more related to your OS and your filesystem: https://www.google.com/search?q=.FileChannelImpl.tryLock+ioexception&ie=utf-8&oe=utf-8

furthermore, i was able to compile it with openjdk12

Hi, yeah that's not the best tool for this as there is a buffer of -n 10000 variants and each time a new variant is read, its is replaced randomly...

with GNU tools: ``` gunzip -c input.vcf.gz | grep '^#' > out.vcf gunzip -c input.vcf.gz | awk -F '\t' 'BEGIN{srand();} /^[^#]/ {printf("%d\t%s\n",int(rand()*100000),$0);}' | sort -T . -t $'\t' -k1,1n |...