fix: ref does not match pileups in example

README.md

@@ -55,7 +55,7 @@ of BAM and FASTA files (`test.sam` and `test.fa`, respectively) are provided.
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	test-mir
 ....>>>>>>>>>>>>>>>>>>>>>>.....................................................	test-mir-5p
 .......................................................>>>>>>>>>>>>>>>>>>>>>...	test-mir-3p
-ATCTCAGCACTTTGAGAGGCCAAAGTGGATGGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACAAGGTGAA	test_ref:3618-3696:+
+GGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTA	test_ref:3618-3696:+
 ACCATGAGGTAGTAGGTTGTATAGTT.....................................................	1
 ..CATGAGGTAGTAGGTTGTATAGTT.....................................................	10
 ..GA-GAGGTAGTAGGTTGTATAGTT.....................................................	2
@@ -111,7 +111,7 @@ Then run the test command above.
 
 In both cases, a successful test run with the above command will create a file
 `test.test-mir.min.1.pileup.tab` in the current working directory with MD5 sum
-`6b5a66981bd83329219002897be393a6`.
+`c9fe3f47da7d73b864823e1fc0636d4c`.
 
 ## Options
 
@@ -168,7 +168,8 @@ In both cases, a successful test run with the above command will create a file
 
 To create a BGZIP-compressed copy of your reference file in FASTA format, as
 required by option `--reference`, you will need the `bgzip` utility that comes
-with the [HTSlib][htslib] suite.
+with the [HTSlib][htslib] suite. If you have have installed dependencies via
+Conda, then the HTSlib suite will be already installed.
 
 Supposing you have HTSlib installed and have a reference file `test.fa` in
 your current working directory, you can create a BGZIP-compressed copy of it

ascii_alignment_pileup.R

@@ -29,7 +29,7 @@ against one or more regions specified in a BED file.\n"
 author <- "Author: Alexander Kanitz"
 affiliation <- "Affiliation: Biozentrum, University of Basel"
 email <- "Email: alexander.kanitz@alumni.ethz.ch"
-version <- "1.1.0"
+version <- "1.1.1"
 version_formatted <- paste("Version:", version, sep=" ")
 requirements <- c("optparse", "rtracklayer", "GenomicAlignments", "tools")
 requirements_txt <- paste("Requires:", paste(requirements, collapse=", "), sep=" ")

environment.yml

@@ -5,3 +5,4 @@ channels:
 dependencies:
   - r-optparse=1.7.1
   - bioconductor-rtracklayer=1.54.0
+  - tabix=1.11

tests/expected_output.md5

-6b5a66981bd83329219002897be393a6  test.test-mir.min.1.pileup.tab
+c9fe3f47da7d73b864823e1fc0636d4c  test.test-mir.min.1.pileup.tab

tests/test_files/test.test-mir.min.1.pileup.tab

 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	test-mir
 ....>>>>>>>>>>>>>>>>>>>>>>.....................................................	test-mir-5p
 .......................................................>>>>>>>>>>>>>>>>>>>>>...	test-mir-3p
-ATCTCAGCACTTTGAGAGGCCAAAGTGGATGGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACAAGGTGAA	test_ref:3618-3696:+
+GGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTA	test_ref:3618-3696:+
 ACCATGAGGTAGTAGGTTGTATAGTT.....................................................	1
 ..CATGAGGTAGTAGGTTGTATAGTT.....................................................	10
 ..GA-GAGGTAGTAGGTTGTATAGTT.....................................................	2