added random gene list for negative controls

core-w/2020-10-18_makeIndex.sh

@@ -176,6 +176,7 @@ vsec "Your output directory is ${outputDirectory}"
 export od=${outputDirectory}
 export matureSamMerge="${od}/matureSamMerge"
 export wptIdx="${od}/whippetIndex"
+export fqd="${od}/whippetFASTQ";
 
 # validate threadCount
 ssec "proceeding with ${threadCount} threads"
@@ -216,13 +217,20 @@ main() {
     makeWhippetIndex || die "unable to prepare whippet index"
   fi
 
+  # generate whippet index
+  if [ "$nm" -lt "4" ]
+  then
+    echo "Preparing to analyse cytoplasmic alignments"
+    generateSequence || die "unable to prepare whippet index"
+  fi
+
   die "no further instructions provided"
 }
 
 
 ####################################
 
-# generate on the fly whippet index using mature bams
+# merge cytoplasmic bams and prepare to make whippet index
 function prepareForWhippetIndex() {
 
   nsec "preparing cytoplasmic alignments for whippet indexing"
@@ -242,7 +250,7 @@ function prepareForWhippetIndex() {
     ssec "Output for already exists and was last modified at ${mergedFileModDate} --- Returning"
     export returnWhippet="1"
   fi
-  [ ${returnWhippet} == "1" ] && return 0
+  [ "${returnWhippet}" -eq "1" ] && return 0
 
   # tell bash to die if an undefined variable is used
   set -u
@@ -286,7 +294,7 @@ function prepareForWhippetIndex() {
     cd ${splitMerged} || die "1"
     samtools rmdup -S ${myBam} - > ${myBam%.bam}.unique.bam || die "2"
     rm ${myBam} 2>/dev/null || die "could not remove ${myBam}"
-    rm ${myBam%.}.bai 2>/dev/null || die "could not remove ${myBam%.}.bai"
+    rm ${splitMerged}/${myBam%.*}.bai 2>/dev/null #|| die "could not remove ${myBam%.*}.bai"
   }; export -f removeBamDup
 
   # call the function for each bam
@@ -324,9 +332,11 @@ function makeWhippetIndex() {
 
   # make an output directory for whippet
   mkdir -p ${wptIdx} 2>/dev/null
-  cd ${wptIdx} || die "cannot access whippet index directory"; rm -rf ${wptIdx}/*
-  julia ${whippetPath}/whippet-index.jl --fasta "${myFasta}" --bam "${matureSamMerge}/unique.sorted.merged.bam" --gtf "${myAnnotation}" --bam-min-reads 3  --index ${wptIdx} || die "canot make whippet index"
-
+  cd ${wptIdx} || die "cannot access whippet index directory"
+  rm -rf ${wptIdx}/* # clear the index
+  ssec "launching whippet"
+  julia ${whippetPath}/whippet-index.jl --fasta "${myFasta}" --bam "${matureSamMerge}/unique.sorted.merged.bam" --gtf "${myAnnotation}" --bam-min-reads 3  --index "${od}/whippetIndex/index_" || die "canot make whippet index"
+  ssec "succesfully build whippet index"
 }
 
 ####################################
@@ -337,7 +347,7 @@ function generateSequence() {
   nsec "generating sequences for each cytoplasmic alignment"
 
   # make fastq directory
-  export fqd="${od}/whippetFASTQ"; mkdir -p ${fqd} 2>/dev/null;
+  mkdir -p ${fqd} 2>/dev/null;
   [ -d ${fqd} ] || die "cannot access fqd"
 
   # define a function, fetchFastq, to fetch the fastq for each alignment in the user-provided cytoplasmic alignment folder