.functions

### Mount with sshfs
connect () { 
    $HOME/.dotfiles/.connect
    }

### Make and cd into directory
mcd () {
    mkdir -p $1
    cd $1
    }

### Decompress from any format
extract () {
   if [ -f $1 ] ; then
       case $1 in
        *.tar.bz2)      tar xvjf $1 ;;
        *.tar.gz)       tar xvzf $1 ;;
        *.tar.xz)       tar Jxvf $1 ;;
        *.bz2)          bunzip2 $1 ;;
        *.rar)          unrar x $1 ;;
        *.gz)           gunzip $1 ;;
        *.tar)          tar xvf $1 ;;
        *.tbz2)         tar xvjf $1 ;;
        *.tgz)          tar xvzf $1 ;;
        *.zip)          unzip $1 ;;
        *.Z)            uncompress $1 ;;
        *.7z)           7z x $1 ;;
        *)              echo "don't know how to extract '$1'..." ;;
       esac
   else
       echo "'$1' is not a valid file!"
   fi
}

### Show numbered column names
getcols() {
    if [ -f $1 ]; then
        grep -v '^#' $1 | awk 'NR==1{for (i=1; i<=NF; i++) print i"|"$i}'
    else
        echo "'$1' is not a valid file!"
    fi
}

# Readlink
function readlink() {
  DIR=$(echo "${1%/*}")
  (cd "$DIR" && echo "$(pwd -P)")
}


### Open Facets PNG from cluster
open_facets() {
        SSTRING=$1
        FLIST=$(ls -t /ifs/res/taylorlab/impact_facets/facets_0.5.14/manifests/impact_facets_manifest*txt | cut -f1 | head -1)

        MATCHES=$(grep "$SSTRING" $FLIST | cut -f2 | sort | uniq | wc -l)
        if [ "$MATCHES" -gt 1 ]
        then
                echo "More than one match, specify sample"
                return 1
        fi

        if [ "$MATCHES" -eq 0 ]
        then
                echo "No matches"
                return 1
        fi

        SPATH=$(grep "$SSTRING" $FLIST | head -1)
        SAMPLE=$(echo $SPATH | tr " " "\t" | cut -f2)
        echo "Opening $SAMPLE"

        SPATH=$(ls $(echo $SPATH | tr " " "\t" | cut -f8)*purity.CNCF.png)
        echo "Path: $SPATH"
        open $SPATH
}

# Get url to 12-245 bam file
bam_url() {
        BASE=$1
        grep $BASE ~/luna/keys/key.txt | \
                cut -f1,2 -d"," | \
                sed -e 's:,:    /ifs/dmpshare/share/irb12_245/:g' \
                -e 's/$/.bam/g'
}