Pierre Lindenbaum

FYI: changing pair1 in the test arityString() produces an error: ```diff diff --git a/src/test/java/com/beust/jcommander/JCommanderTest.java b/src/test/java/com/beust/jcommander/JCommanderTest.java index a9360ea..877238b 100644 --- a/src/test/java/com/beust/jcommander/JCommanderTest.java +++ b/src/test/java/com/beust/jcommander/JCommanderTest.java @@ -189,13 +189,14 @@ public class JCommanderTest {...

>? you mean you want to avoid argument list too long error or something? yes. Something like what the broad is doing with the '.list' suffix: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_engine_CommandLineGATK.php#--input_file > An input...

> Can I transfer only a range of bytes from my remote location and then use those bytes to get a SAMFileHeader? yes just open a URL, open a SAMreader...

@gariem well, you'll only download the first bytes will the method above, not the whole bam.

as far as I know the max length of a chromosome is max(int32)= 2,147,483,647 so there shouldn't have any problem on this side. There may be a problem when you're...

there was a project [samtools/htsjdk-next-beta](https://github.com/samtools/htsjdk-next-beta/) which aim was to implement long REFs (eg.: https://github.com/samtools/htsjdk-next-beta/pull/6 ) . But the project looks inactive (dead ?) now.

@bioinfornatics you can try to use a VCFIteratorBuilder instead of a VCFFileReader . As far as I remember, the GZ compression was first tested. (But you cannot do random-access)

@cmnbroad well it should be possible as you can get this information with `bcftools index -s in.vcf.gz`

@yfarjoun with a recent version of bcftools, I'm able to extract the number of variants/chrom with a **tbi** index and `bcftools index -s`.

@yfarjoun bcftools. (but I think now both tools now use the same C code for tbi )