How to enable --pileup mode/feature?

statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

Apache License 2.0

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How to enable --pileup mode/feature? #19

Open papanikos opened 6 years ago

papanikos commented 6 years ago

Thanks for the pointer in #14 !

However, when I try to activate this mode like the following, I get an error:

$demuxlet --pileup \
--sam /path/to/bam \
--field GT --geno-error 0.01 \
--sm-list samples.txt \
--group-list barcodes.tsv \
--out out_prefix \
--alpha 0 --alpha 0.5

---output truncated---

FATAL ERROR - 
[E:params.cpp:564 Status] Problems encountered parsing command line:

Command line parameter --pileup (#1) not recognized

terminate called after throwing an instance of 'pException'
  what():  Exception was thrown
Aborted (core dumped)

Thank you in advance!

yimmieg commented 6 years ago

ah sorry, this is currently still in beta. will hopefully be updated soon...

ToledoEM commented 6 years ago

Any update for this feature, at least to replicate the function used in the manuscript.

hyunminkang commented 6 years ago

pileup function is not related to replication of the manuscript

On Fri, Jun 15, 2018 at 2:25 AM Enrique Toledo M. notifications@github.com wrote:

Any update for this feature, at least to replicate the function used in the manuscript.

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