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Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $2 @@ -182,18 +183,26 @@ hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" echo "$hasReplicateColumn" #if its a 'new' merged file with replicate info -if [[ "$hasReplicateColumn" == "Yes" ]] ; then - echo "
" >> $outputFile
+if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then
+ if [[ "${clonality_method}" == "boyd" ]] ; then
+ echo "
" >> $outputFile
+ else
+ echo "
" >> $outputFile
+ fi
+
for sample in $samples; do
echo "${clonality_method}"
if [[ "${clonality_method}" == "old" ]] ; then
echo "in old"
clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
echo "" >> $outputFile
- echo "
| Clonality Score: $clonalityScore | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Clonality Score: $clonalityScore | |||||||||||||||
| Replicate ID | Number of Reads | ||||||||||||||
| Replicate ID | Number of Sequences | ||||||||||||||
| $replicate | $reads | ||||||||||||||
| Coincidence Type | Raw Coincidence Freq | ||||||||||||||
| Number of replicates containing the coincidence | Number of sequences shared between replicates | ||||||||||||||
" >> $outputFile
+
echo "| Sample | count | V.DEL | P1 | N1 | P2 | DEL.D | D.DEL | P3 | N2 | P4 | DEL.J | Total.Del | Total.N | Total.P | Median.CDR3 |
|---|