quick_functions.sh

#!/bin/bash

# set some global variables for convenience
[ -d "$HOME/Documents/conf/FamilyR13" ] && CONF="$HOME/Documents/conf" || CONF=/confidential
export SVCOMPARE="$CONF/FamilyR13/DATA/10x/sv_compare"
export FILTERED_VCFS="$SVCOMPARE/17-08_hg38/filtered_vcfs-BK/"
#export PBBAM="$CONF/iGenVar/Chromothripsis/PacBio-Chromothripsis/aligned_bam/17-08/m64080_191203_205633.minimap2.GRCh38.sorted.bam"
export PBBAM="$CONF/tGenVar/tech/pb/bamIndex/pb.17_08.hg38.bam"
export PBBAM_IDX="$CONF/tGenVar/tech/pb/bamIndex/pb.17_08.hg38.bam.bai"
export REFHG38="$CONF/FamilyR13/DATA/REF/GRCh38_hengli_recommended/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
export REFT2T="$CONF/tGenVar/ref/t2t_v1.1/chm13.draft_v1.1.fasta"
export T2T="$CONF/tGenVar/tech/pb/bam_MDtag_t2tv1_1/pb.17_08.t2tv1_1.bam"
export T2T_IDX="$CONF/tGenVar/tech/pb/bam_MDtag_t2tv1_1/pb.17_08.t2tv1_1.bam.bai"
export ILL_HG38="$CONF/tGenVar/tech/illumina/bam_hg38/ill.17_08.hg38.bam"
#export T2T="$CONF/iGenVar/Chromothripsis/PacBio-Chromothripsis/aligned_bam/17-08/m64080_191203_205633.minimap2.T2T.sorted.bam"
#export T2T_IDX="$CONF/tGenVar/tech/pb/bam_t2t/pb.17_08.t2t.bam.bai"
VCFSSUFFIX="_sorted_filtered.vcf.gz"

getmethod() {
    METHOD=$(echo $1 | awk -F_ '{print $1}')
    [[ $METHOD =~ "audano" ]] && METHOD="audano"
    echo "$METHOD"
}

getvar() {
    # get method
    METHOD="$(getmethod $1)"

    # get variant line
    SVSUFFIX=${1#*_}
    zgrep "${METHOD}_${SVSUFFIX}" "${FILTERED_VCFS}/${METHOD}${VCFSSUFFIX}"
}

getpos() {
        getvar $1 | cut -f1,2 | tr "\t" ":"
}

find_in_bam() {
    # find_in_bam read_id bamfile [bamIndex] chromosome
    if [[ "$3" =~ .*bai ]]
    then
        samtools view "$2" -X "$3" "$4" -@8 | grep "$1"
    else
        samtools view "$2" "$3" -@8 | grep "$1"
    fi
}

hg38_read() {
    find_in_bam "${1}" "${PBBAM}" "${PBBAM_IDX}" "${2}" | head -n1
}

t2t_read() {
    find_in_bam "${1}" "${T2T}" "${T2T_IDX}" "${2}" | head -n1
}