Miika Ahdesmaki

Unit tests were fine when I compiled gossamer. I ran several samples yesterday and all showed the same behaviour. Here's the ls output: ``` ls -l dna/SRR1176814*.gz -rw-rw-r-- 1 ubuntu...

As this is all public data, if you're interested you can download the fastq.gz files here https://www.ebi.ac.uk/ena/data/view/SRR1176814 It looks like all the output fastq files are correctly produced though so...

Hi @gt1, cheers for the quick reply. The colleague running this analyses just nuked the work folder and went for just aligning the samples each in one go (instead of...

Hi @pjotrp, thanks for looking into this, happy to provide an example. Say I wanted to get tab-delimited output from vcf in the following way: `zcat my.vcf.gz | bio-vcf --sfilter...

Certainly, the two below variants will have different numbers of fields due to one having more stuff in `KNOWN` ``` chr11 69465986 76 N . PASS AC=0;AN=0;ANN=|frameshift_variant&stop_lost|HIGH|CCND1|CCND1|transcript|NM_053056.2|Coding|5/5|c.825_*415del|p.Glu275fs|1034/4289|825/888|275/295||,|3_prime_UTR_variant|MODIFIER|CCND1|CCND1|transcript|NM_053056.2|Coding|5/5|c.825_*415del||||||;CIEND=-352,10;CIEND95=-58,0;CIPOS=-6,296;CIPOS95=0,58;END=69466465;IMPRECISE;KNOWN=CCND1;LOF=(CCND1|CCND1|1|1.00);PE=6;SIMPLE_ANN=DEL|FRAMESHIFT_VARIANT&STOP_LOST|CCND1|NM_053056.2|,DEL|3_PRIME_UTR_VARIANT|CCND1|NM_053056.2|;SR=0;STRANDS=+-:6;SU=6;SVLEN=-479;SVTYPE=DEL GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:RP:AP:AB 0/0:6:6:0:200.0:0.0:-3.0,-247.0,-825.0:830:828:1:828:1:0:0:828:1:0.0012 chr12...

Hi @pjotrp Thanks for the feedback again. I've tried the above `.join(",")` solution but it falls apart when there is only one entry (or no entries) as strings do not...

Thanks - I know ruby very little but could I write a little function before the brackets that would do the join (or not do the join) on multiple of...

Nice, thanks, I'll give that a go

This seems to have done it for me: `f=lambda{|x| ( x.nil? ? "" : (x.kind_of?(String) ? x : x.join(","))) } ;`

Thanks for the comments - will the statically linked target still depend on quite a new libc though if you compile it on Ubuntu 16?