fix(scripts): Wire entrypoint to central dispatch

scripts/arcasHLA.py already centralizes arg parsing and dependency
checks, but the top-level `arcasHLA` wrapper still hand-rolled its own
per-command dispatch and ad-hoc dependency warnings. Forward all
invocations to the central dispatch script instead.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: jonasfreimuth

arcasHLA

@@ -13,94 +13,14 @@
 #   arcasHLA types high resolution HLA alleles from BAM.
 #
 #-----------------------------------------------------------------------------
-#   Requirements
+#   Dispatch
 #-----------------------------------------------------------------------------
-
-if [ ! -x "$(command -v kallisto pseudo)" ]; then
-    echo "Warning: missing dependency - Kallisto v0.44.0"
-fi
-
-if [ ! -x "$(command -v samtools)" ]; then
-    echo "Warning: missing dependency - Samtools"
-fi
-
-if [ ! -x "$(command -v bedtools)" ]; then
-    echo "Warning: missing dependency - bedtools"
-fi
-
-if [ ! -x "$(command -v pigz)" ]; then
-    echo "Warning: missing dependency - pigz"
-fi
-
-if [ ! -x "$(command -v python3 -c "import numpy")" ]; then
-    echo "Warning: missing dependency - python3 module NumPy"
-fi
-
-if [ ! -x "$(command -v python3 -c "import pandas")" ]; then
-    echo "Warning: missing dependency - python3 module pandas"
-fi
-
-if [ ! -x "$(command -v python3 -c "import Bio")" ]; then
-    echo "Warning: missing dependency - python3 module Biopython"
-fi
-
-#-----------------------------------------------------------------------------
-#   Tools
+#
+#   Argument parsing, tool dependency checks and subcommand dispatch are all
+#   handled by scripts/arcasHLA.py, so this wrapper just forwards to it.
 #-----------------------------------------------------------------------------
 
 ARCASHLA_ROOT_DIR=$(realpath $(dirname $0))
 
-if [ "$1" == "extract" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/extract.py ${@:2}
-
-elif [ "$1" == "genotype" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/genotype.py ${@:2}
-
-elif [ "$1" == "merge" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/merge.py ${@:2}
-
-elif [ "$1" == "reference" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/reference.py ${@:2}
-
-elif [ "$1" == "partial" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/partial.py ${@:2}
-    
-elif [ "$1" == "customize" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/customize.py ${@:2}
-
-elif [ "$1" == "quant" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/quant.py ${@:2}
-
-elif [ "$1" == "convert" ]; then
-
-    python3 ${ARCASHLA_ROOT_DIR}/scripts/convert.py ${@:2}
-    
-#-----------------------------------------------------------------------------
-#   Usage
-#-----------------------------------------------------------------------------
-
-else
-    echo "Usage: arcasHLA <command> [options]"
-    echo
-    echo "    extract        extracts chromosome 6 reads from bam"
-    echo "    genotype       types HLA genes from extracted reads"
-    echo "    partial        types partial HLA genes from extracted reads"
-    echo
-    echo "    customize      create custom HLA reference"
-    echo "    quant          allele specific HLA quantification"
-    echo
-    echo "    merge          processes results into a tab-separated table"
-    echo "    convert        converts HLA nomenclature/resolution"
-    echo "    reference      check or update HLA reference"
-    echo 
-    echo "Note: run any command with --help to view required fields, options"
-    echo
-fi
+python3 ${ARCASHLA_ROOT_DIR}/scripts/arcasHLA.py "$@"
 #-------------------------------------------------------------------------------