docs: fix CLI usage in examples (#5)

clintval · Jul 26, 2024 · 46022f2 · 46022f2
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diff --git a/README.md b/README.md
@@ -37,20 +37,20 @@ Although paired-end reads will give the most discriminatory power for disambigua
 - Will disambiguate an arbitrary number of BAMs, all aligned to different references
 - Writes the ambiguous alignments to a separate directory
 - Extensible implementation which supports alternative disambiguation strategies
-- Benchmarks show high accuracy: [Click Here](benchmarks/disambiguate.md)
+- Benchmarks show high accuracy: [Click Here](benchmarks/README.md)
 
 ### Command Line Usage
 
 ```bash
-❯ neodisambiguate -i infile1.bam infile2.bam -p out/disambiguated
+❯ neodisambiguate -i infile1.bam infile2.bam -o out/disambiguated
 ```
 
 ### Example Usage
 
 To disambiguate templates for sample `dna00001` that are aligned to human (A) and mouse (B):
 
 ```bash
-❯ neodisambiguate -i dna00001.A.bam dna00001.B.bam -p out/dna00001 -n hg38 mm10
+❯ neodisambiguate -i dna00001.A.bam dna00001.B.bam -o out/dna00001 -n hg38 mm10
 ```
 
 ```console

diff --git a/benchmarks/disambiguate.md → benchmarks/README.md b/benchmarks/disambiguate.md → benchmarks/README.md
diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala
@@ -120,7 +120,7 @@ object Disambiguate {
          |To disambiguate a sample aligned to human (A) and mouse (B):
          |
          |```
-         |❯ neodisambiguate -i dna00001.A.bam dna00001.B.bam -p out/dna00001 -n hg38 mm10
+         |❯ neodisambiguate -i dna00001.A.bam dna00001.B.bam -o out/dna00001 -n hg38 mm10
          |
          |❯ tree out/
          |  out/