#!/bin/bash -Ceuo pipefail
if [ -n "chr6_GL000251v2_alt" ]; then
    tabix -h 1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz chr6_GL000251v2_alt > input_filtered.vcf
    bgzip input_filtered.vcf
    input_vcf="input_filtered.vcf.gz"
else
    input_vcf="1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.merged.vcf.gz"
fi

whatshap \
    phase \
     \
    --reference Homo_sapiens_assembly38.fasta \
    -o 1029_01F-T1-TDNA-1_A23TNVYLT4_1_vs_1029_01F-N1-BDNA-1_B23KFG5LT4_1.snv_indel.whatshap.chr6_GL000251v2_alt.phased.vcf.gz \
    $input_vcf \
    1029_01F-T1-TDNA-1_A23TNVYLT4_1.recalibrated.bam

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_SOMATIC_SNV_INDEL:WHATSHAP":
    whatshap: $(whatshap --version)
END_VERSIONS