Test --mcs

ksahlin · Oct 7, 2024 · fc34ebf · fc34ebf
1 parent 2491b3d
commit fc34ebf
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diff --git a/tests/phix.mcs.se.paf b/tests/phix.mcs.se.paf
@@ -0,0 +1,11 @@
+SRR1377138.32	301	2	293	+	NC_001422.1	5386	1434	1725	47	291	255
+SRR1377138.33	301	2	297	+	NC_001422.1	5386	3818	4113	47	295	255
+SRR1377138.34	301	33	299	-	NC_001422.1	5386	844	1110	40	266	255
+SRR1377138.35	301	5	298	-	NC_001422.1	5386	4041	4334	47	293	255
+SRR1377138.36	301	3	301	+	NC_001422.1	5386	4997	5295	51	298	255
+SRR1377138.37	301	2	299	-	NC_001422.1	5386	794	1091	42	297	255
+SRR1377138.38	301	32	284	-	NC_001422.1	5386	4971	5223	42	252	255
+SRR1377138.39/1	301	1	295	-	NC_001422.1	5386	1791	2085	48	294	255
+SRR1377138.40	301	4	293	-	NC_001422.1	5386	3020	3309	44	289	255
+rescuable.42	301	4	293	-	NC_001422.1	5386	3020	3309	44	289	255
+not.rescuable	301	4	293	-	NC_001422.1	5386	3020	3309	44	289	255
diff --git a/tests/run.sh b/tests/run.sh
@@ -116,4 +116,9 @@ strobealign --no-PG --eqx --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fa
 diff tests/phix.se.sam multiblock.sam
 rm multiblock.fastq.gz multiblock.sam
 
+# Single-end PAF with multi-context seeds
+strobealign --mcs -x tests/phix.fasta tests/phix.1.fastq | tail -n 11 > phix.mcs.se.paf
+diff tests/phix.mcs.se.paf phix.mcs.se.paf
+rm phix.mcs.se.paf
+
 echo "Success"