bug fix

telatin · Dec 21, 2022 · 8e260f6 · 8e260f6
1 parent 8e82573
commit 8e260f6
Showing 1 changed file with 38 additions and 2 deletions.
diff --git a/test/test-tab.sh b/test/test-tab.sh
@@ -63,12 +63,48 @@ fi
 
 
 ## FASTA SE
-FA_LINES=$(getnumber $("$BINDIR"/seqfu tabulate "$FILES"/comments.fasta | SEQFU_QUIET=1 "$BINDIR"/seqfu tabulate -d | wc -l))
+FA_LINES=$(getnumber "$("$BINDIR"/seqfu tabulate "$FILES"/comments.fasta | SEQFU_QUIET=1 "$BINDIR"/seqfu tabulate -d | wc -l)")
 
 if [[ $FA_LINES == "8" ]]; then
     echo -e "$OK: FASTA output format: $FA_LINES"
     PASS=$((PASS+1))
 else
     echo -e "$FAIL: FASTA output format: 8 expected, got $FA_LINES"
     ERRORS=$((ERRORS+1))
-fi
+fi
+
+## Pair end?
+
+TEMPORARY_DIR=$(mktemp -d)
+"$BINDIR"/seqfu tabulate -i "$FILES"/interleaved.fq.gz > "$TEMPORARY_DIR"/interleaved.tabcheck
+EXP=8
+GOT=$(getnumber "$("$BINDIR"/fu-tabcheck "$TEMPORARY_DIR"/interleaved.tabcheck | cut -f 3)")
+if [[ $GOT == "$EXP" ]]; then
+    echo -e "$OK: Tabulated file has $EXP columns: $GOT"
+    PASS=$((PASS+1))
+else
+    echo -e "$FAIL: Tabulated file has not $EXP columns: $GOT"
+    ERRORS=$((ERRORS+1))
+fi
+
+"$BINDIR"/seqfu tabulate -d "$TEMPORARY_DIR"/interleaved.tabcheck| "$BINDIR"/seqfu deinterleave -o  "$TEMPORARY_DIR"/dei -
+EXP=7
+GOT=$(getnumber "$("$BINDIR"/seqfu cnt -u "$TEMPORARY_DIR"/dei_R1.fq | cut -f 2)")
+if [[ $GOT == "$EXP" ]]; then
+    echo -e "$OK: Deinterleaved detabulated has $EXP R1 reads: $GOT"
+    PASS=$((PASS+1))
+else
+    echo -e "$FAIL: Deinterleaved detabulated has not $EXP R1 reads: $GOT"
+    ERRORS=$((ERRORS+1))
+fi
+
+GOT=$(getnumber "$("$BINDIR"/seqfu cnt -u "$TEMPORARY_DIR"/dei_R2.fq | cut -f 2)")
+if [[ $GOT == "$EXP" ]]; then
+    echo -e "$OK: Deinterleaved detabulated has $EXP R2 reads: $GOT"
+    PASS=$((PASS+1))
+else
+    echo -e "$FAIL: Deinterleaved detabulated has not $EXP R2 reads: $GOT"
+    ERRORS=$((ERRORS+1))
+fi
+rm -rf "$TEMPORARY_DIR"
+