BR='
'
+unescape() {
+ local unescape='s;(^(\\\\)*|[^\\](\\\\)*)\\n;\1\n;g; s;\\(.);\1;g'
+ if [ $# -eq 0 ]; then
+ sed -E "$unescape"
+ else
+ printf %s "$*" \
+ | sed -E "$unescape"
+ fi
+}
+
pdi_load() {
# normalise PDI file for processing with pdi_* functions
# functions in this library can only be applied to normalised data
# Usage example:
# data="$(pdi_load file.vcf)"
- sed -En '
+ sed -srn '
# === Read entire file into buffer ===
:X $bY; N; bX; :Y s;^.*$;\n&\n;;
# === Unscramble aggregated fields ===
:disag
- s;\n([^:]+:)((.*[^\])?(\\\\)*),;\n\1\2\n\1;;
+ s;\n([^:\n]+:)(([^\n]*[^\])?(\\\\)*),;\n\1\2\n\1;;
t disag;
# === Insert FN when only N is present ===
# === Update obsolete LABEL property ===
s;\nLABEL((\;[A-Za-z0-9-]+|\;[A-Za-z0-9-]+=([^;,:"]+|"[^"]+")(,[^;,:"]+|,"[^"]+")*)*):(.*)\n;\nADR\1\;LABEL="\5":\n;g;
- p;' "$1"
+ p;' "$@"
}
pdi_count(){
}
pdi_attrib(){
- local card=":$1" name="$2" cnt="${3:-1}"
+ local card=":$1" name="$2" cnt="${3:-1}" attr="$4"
while [ $cnt -gt 0 ]; do
[ "${card#*${BR}${name};}" = "$card" ] && return 1
card="${card#*${BR}${name};}"
cnt=$((cnt - 1))
done
- printf %s\\n "${card%%:*}"
+ card="${card%%:*}"
+ if [ "$attr" ]; then
+ case $card in
+ *\;"$attr"=*) card="${card#*;${attr}=}";;
+ "$attr"=*) card="${card#${attr}=}";;
+ "$attr"|*\;"$attr"|"$attr"\;*|*\;"$attr"\;*) return 0;;
+ *) return 1;;
+ esac
+ case $card in
+ \"*\"\;*|\'*\'\;*)
+ card="${card#[\"\']}"; card="${card%%[\"\'];*}"
+ ;;
+ \"*\"|\'*\')
+ card="${card#[\"\']}"; card="${card%%[\"\']}"
+ ;;
+ *\;*) card="${card%%;*}";;
+ esac
+ fi
+ printf %s\\n "${card}"
}
pdi_value(){