###############################################################################
# README file for how the calling regions for the single-sample HC based
# exome calling pipeline were created.  The following is a two-part process
# of identifying and formating various input sets of calling regions and then
# secondarily combining and padding said regions.
###############################################################################

# ===============================================
# =============== gencode.v19.il ================
# ===============================================
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
cp $hg19/Homo_sapiens_assembly19.dict tmp.il
zcat gencode.v19.annotation.gtf.gz | awk '$3 == "CDS" {if ($1=="chrM") chr="MT"; else chr=$1; print chr, $4, $5, $7, $18}' | tr ' ' '\t' | sed 's/chr//' | tr -d '";' >> tmp.il
java -jar ~tfennell/bin/IntervalListTools.jar I=tmp.il O=gencode.v19.il UNIQUE=true
rm tmp.il


# ===============================================
# =============== mirbase.v20.il ================
# ===============================================
wget -O mirbase.v20.gff ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3
cp $hg19/Homo_sapiens_assembly19.dict tmp.il
cat mirbase.v20.gff | awk '$3 == "miRNA_primary_transcript" {sub(/chr/,"",$1); sub(/M/, "MT", $1); sub(/.*Name=/, "", $9); print $1,$4,$5,$7,$9}' | tr ' ' '\t' >> tmp.il
java -jar ~tfennell/bin/IntervalListTools.jar I=tmp.il O=mirbase.v20.il UNIQUE=true
rm tmp.il


# ===============================================
# ============= illumina_exome.il ===============
# ===============================================
cp $hg19/Homo_sapiens_assembly19.dict tmp.il
egrep -v '^@' /seq/references/HybSelOligos/whole_exome_illumina_coding_v1/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list \
    | awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $4, "ice_target_" FNR}' >> tmp.il
java -jar ~tfennell/bin/IntervalListTools.jar I=tmp.il O=ice_coding_v1_targets.il UNIQUE=true
rm tmp.il

# ===============================================
# ======= Put it all together and pad it ========
# ===============================================
java -jar ~tfennell/bin/IntervalListTools.jar I=gencode.v19.il I=mirbase.v20.il I=ice_coding_v1_targets.il UNIQUE=true PADDING=50 O=exome_calling_regions.v1.interval_list