Update test 1 and test data, fix some arg types in config and script

src/umi_tools/umi_tools_dedup/config.vsh.yaml

@@ -134,7 +134,7 @@ argument_groups:
           tags are “NH”, “X0” and “XT”. If not specified, the read with the highest
           mapping quality will be selected.
       - name: --read_length
-        type: integer
+        type: boolean_true
         description: |
           Use the read length as a criteria when deduping, for e.g sRNA-Seq.
   

src/umi_tools/umi_tools_dedup/help.txt

@@ -33,15 +33,13 @@ Dedup Options:
       --output-stats=<prefix>             One can use the edit distance between UMIs at the same position as an quality control for the 
                                           deduplication process by comparing with a null expectation of random sampling. For the random
                                           sampling, the observed frequency of UMIs is used to more reasonably model the null expectation.
-
+                                          Use this option to generate a stats outfiles called: 
+                                                [PREFIX]_stats_edit_distance.tsv   
+                                                      Reports the (binned) average edit distance between the UMIs at each position.
                                           In addition, this option will trigger reporting of further summary statistics for the UMIs which
                                           may be informative for selecting the optimal deduplication method or debugging.
                                           Each unique UMI sequence may be observed [0-many] times at multiple positions in the BAM. The
                                           following files report the distribution for the frequencies of each UMI.
-
-                                          Use this option to generate a stats outfiles called: 
-                                                [PREFIX]_stats_edit_distance.tsv   
-                                                      Reports the (binned) average edit distance between the UMIs at each position.
                                                 [PREFIX]_stats_per_umi_per_position.tsv
                                                       Tabulates the counts for unique combinations of UMI and position.
                                                 [PREFIX]_stats_per_umi_per.tsv

src/umi_tools/umi_tools_dedup/script.sh

@@ -20,7 +20,7 @@ test_dir="${metal_executable}/test_data"
 [[ "$par_subset" == "false" ]] && unset par_subset
 [[ "$par_log2stderr" == "false" ]] && unset par_log2stderr
 [[ "$par_get_output_stats" == "false" ]] && unset par_get_output_stats
-
+[[ "$par_read_length" == "false" ]] && unset par_read_length
 
 umi_tools dedup \
     --stdin "$par_input" \
@@ -43,7 +43,7 @@ umi_tools dedup \
     ${par_spliced_is_unique:+--spliced-is-unique} \
     ${par_soft_clip_threshold:+--soft-clip-threshold "$par_soft_clip_threshold"} \
     ${par_multimapping_detection_method:+--multimapping-detection-method "$par_multimapping_detection_method"} \
-    ${par_read_length:+--read-length "$par_read_length"} \
+    ${par_read_length:+--read-length} \
     ${par_per_gene:+--per-gene} \
     ${par_gene_tag:+--gene-tag "$par_gene_tag"} \
     ${par_assigned_status_tag:+--assigned-status-tag "$par_assigned_status_tag"} \

src/umi_tools/umi_tools_dedup/test.sh

@@ -7,27 +7,45 @@ mkdir -p "$out_dir"
 
 ############################################################################################
 
-echo ">>> Test 1: Basic usage of $meta_functionality_name"
+echo ">>> Test 1: Basic usage of $meta_functionality_name with statistics output"
 
 "$meta_executable" \
   --paired \
   --input "$test_dir/sample.bam" \
   --bai "$test_dir/sample.bam.bai" \
-  --output "$out_dir/deduped.bam"
+  --output "$out_dir/deduped.bam" \
+  --output_stats deduped \
+  --random_seed 1
 
 echo ">>> Checking whether output exists"
 [ ! -f "$out_dir/deduped.bam" ] && echo "File 'deduped.bam' does not exist!" && exit 1
+[ ! -f "$out_dir/deduped_edit_distance.tsv" ] && echo "File 'deduped_edit_distance.tsv' does not exist!" && exit 1
 
 echo ">>> Checking whether output is non-empty"
 [ ! -s "$out_dir/deduped.bam" ] && echo "File 'deduped.bam' is empty!" && exit 1
+[ ! -s "$out_dir/deduped_edit_distance.tsv" ] && echo "File 'deduped_edit_distance.tsv' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
 diff "$out_dir/deduped.bam" "$test_dir/deduped.bam" || \
     (echo "Output file deduped.bam does not match expected output" && exit 1)
-
+diff "$out_dir/deduped_edit_distance.tsv" "$test_dir/deduped_edit_distance.tsv" || \
+    (echo "Output file deduped_edit_distance.tsv does not match expected output" && exit 1)
 
 ############################################################################################
 
+echo ">>> Test 2: $meta_functionality_name"
+
+"$meta_executable" \
+  --paired \
+  --input "$test_dir/sample.bam" \
+  --bai "$test_dir/sample.bam.bai" \
+  --output "$out_dir/deduped.bam" \
+  --random_seed 1 \
+
+
+echo ">>> Checking whether output exists"
+[ ! -f "$out_dir/deduped.bam" ] && echo "File 'deduped.bam' does not exist!" && exit 1
+[]
 rm -rf "$out_dir"
 
 echo "All tests succeeded!"

src/umi_tools/umi_tools_dedup/test_data/dedup_edit_distance.tsv

@@ -0,0 +1,5 @@
+unique	unique_null	directional	directional_null	edit_distance
+3	3	4	4	Single_UMI
+0	1	0	0	0
+1	0	0	0	1
+0	0	0	0	2

src/umi_tools/umi_tools_dedup/test_data/dedup_per_umi.tsv

@@ -0,0 +1,6 @@
+UMI	median_counts_pre	times_observed_pre	total_counts_pre	median_counts_post	times_observed_post	total_counts_post
+ACCGGTTTA	74	1	74	74	1	74
+ACTGGTTTC	48	1	48	49	1	49
+AGCGGTTAC	1	1	1	1	1	1
+CCAGGTTCT	1	1	1	1	1	1
+TCTGGTTTC	1	1	1	0	0	0

src/umi_tools/umi_tools_dedup/test_data/dedup_per_umi_per_position.tsv

@@ -0,0 +1,5 @@
+counts	instances_pre	instances_post
+1	3	2
+48	1	0
+49	0	1
+74	1	1

src/umi_tools/umi_tools_dedup/test_data/script.sh

@@ -2,6 +2,7 @@
 
 # Download test data
 wget https://github.com/CGATOxford/UMI-tools/releases/download/v0.2.3/example.bam
-samtools view -b -o sample.bam -s 0.00005 example.bam
-samtools index sample.bam > sample.bam.bai
+# extract 150 reads with a maximum of two reads having the same start position
+samtools view -h example.bam | head -n 150 | samtools view -bS - > sample.bam
+samtools index sample.bam
 rm example.bam