#python scripts/make_tiles.py scripts/test/data/hic_small.tsv -o jsons/tiles -p pos1,pos2 --min-value count --max-value count --importance count
python scripts/make_tiles.py -o jsons/tiles -p pos1,pos2 --min-value count --max-value count --importance count -c pos1,pos2,count --max-zoom 5 data/chr22_100kb.RAWobserved


# Move a newly built page to the gh-pages branch
gulp build; git commit -am "New build"; rm -rf /tmp/dist/; cp -r dist /tmp; git checkout gh-pages; cp -r /tmp/dist/* .; cp demo.html index.html;

## Starting the spark notebook

ipython notebook --profile=pyspark --no-browser

## refGene.txt.gz can be downloaded here:

# This implies that its coordinates are relative to the hg19 assembly

http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz


eval $(ssh-agent)
ssh-add ~/devenv-key.pem
rsync -avz ubuntu@52.32.97.221:/data/refgene-tiles-small/ jsons/tiles

### Sample reads set

samtools view -h  data/GM12878_SRR1658581_10pc_3_R1_hg19.bwt2glob.bam | head -n 65536 | samtools view -Sb > data/65536.bam

### Sample tracks from Encode project

GM12878 cell line RNAseq

https://www.encodeproject.org/experiments/ENCSR000CVT/