Update README.md

README.md

@@ -45,13 +45,10 @@ preprimer convert --input-format varvamp --primer-info varvamp/varvamp_outputfol
 
 Give the fasta as argument `--reference`. If a primer gets multiple hits in the new reference it choose a pair located close to where the primer was located in the old reference, assuming that they do not differ vastly. All alignments are saved in folder {output_folder}/alignment/new_reference.  
 
-
 ```
 preprimer convert --input-format varvamp --primer-info varvamp/varvamp_outputfolder/primers.tsv --output-format artic fasta sts  --output-folder schemes --prefix SINV --reference NC_123456.fasta
 ```
 
-```
-
 The varVAMP primers might contain ambiguous nucleotide characters (not only ATCG) that will be a problem for the aligner. Also an alignment will be made which is located in folder   This software will look for these characters during alignment and promt if they are found.   
 
 If `--force` no prompts will be displayed and
@@ -82,7 +79,7 @@ Output:
 
 The output will be saved in {output_folder}/alignment/mepcr and {output_folder}/alignment/exonerate
 ```
-preprimer align --sts-file test_data/ASFV.sts.tsv --output-format me-pcr exonerate --reference test_data/LR722600.1.fasta --prefix ASFV --output-folder test_output_alignment --force
+preprimer align --sts-file tests/test_data/ASFV.sts.tsv --output-format me-pcr exonerate --reference tests/test_data/LR722600.1.fasta --prefix ASFV --output-folder test_output_alignment --force
 ```
 
 ## Contributing