release version 1.2.0-beta08

Author: mathjeff

README.md

@@ -1,6 +1,6 @@
 # X-Mapper: a fast, accurate aligner for genomic sequences
 
-Download the latest release version here: https://github.com/mathjeff/Mapper/releases/download/1.2.0-beta07/x-mapper-1.2.0-beta07.jar
+Download the latest release version here: https://github.com/mathjeff/Mapper/releases/download/1.2.0-beta08/x-mapper-1.2.0-beta08.jar
 
 Read about the algorithm, plus benchmarking and application in the publication here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03473-7
 

src/main/java/mapper/Main.java

@@ -375,7 +375,7 @@ public static void main(String[] args) throws IllegalArgumentException, FileNotF
     if (queries.size() < 1) {
       usageError("--queries or --paired-queries is required");
     }
-    if (outVcfPath == null && outSamPath == null && outRefsMapCountPath == null && outUnalignedPath == null && outMutationsPath == null || allowNoOutput) {
+    if (outVcfPath == null && outSamPath == null && outRefsMapCountPath == null && outUnalignedPath == null && outMutationsPath == null && !allowNoOutput) {
       usageError("No output specified. Try --out-vcf <output path>, or if you really don't want to generate an output file, --no-output");
     }
     alignmentLogger = new Logger(outputWriter, 1, alignmentVerbosity);