From 831772d443500eaca2bcec25e11751c3c05e988b Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
Date: Sat, 9 Jul 2022 10:20:29 +0200
Subject: [PATCH] test: add test files and docs
---
README.md | 29 +++++++++++++++++++++++++++++
ascii_alignment_pileup.R | 0
tests/test_files/test.bam | Bin 0 -> 1581 bytes
tests/test_files/test.bam.bai | Bin 0 -> 46080 bytes
tests/test_files/test.bed | 1 +
tests/test_files/test.gff | 3 +++
6 files changed, 33 insertions(+)
mode change 100644 => 100755 ascii_alignment_pileup.R
create mode 100644 tests/test_files/test.bam
create mode 100644 tests/test_files/test.bam.bai
create mode 100644 tests/test_files/test.bed
create mode 100644 tests/test_files/test.gff
diff --git a/README.md b/README.md
index 6f00385..54bfd78 100644
--- a/README.md
+++ b/README.md
@@ -69,6 +69,35 @@ TACCATGAGGTAGTAGGTTGTATAGTT.....................................................
.........................................................TATACAATCTACTGTCTTTCCT. 1
```
+## Example
+
+There is a set of test files available in directory `tests/`. If you are in
+the repository root directory, and all dependencies are installed and
+available, you can use the following command to run a test:
+
+```bash
+ascii_alignment_pileup.R \
+ --verbose \
+ --annotations="tests/test_files/test.gff" \
+ --output-directory="$PWD" \
+ "tests/test_files/test.bed" \
+ "tests/test_files/test.bam"
+```
+
+Note that if you build a Docker image from the provided `Dockerfile` or pull
+one of the prebuilt images (see section [Requirements](#requirements)), the
+test files are included in those images. Therefore, you can also run the tests
+in a container. To do that, start a container with:
+
+```bash
+docker run --rm -it <IMAGE_ID> /bin/bash
+```
+
+Then run the test command above.
+
+In both cases, a successful test will create a file
+`test.hsa-let-7a-1.min.1.pileup.tab` in the current working directory.
+
## Options
```console
diff --git a/ascii_alignment_pileup.R b/ascii_alignment_pileup.R
old mode 100644
new mode 100755
diff --git a/tests/test_files/test.bam b/tests/test_files/test.bam
new file mode 100644
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diff --git a/tests/test_files/test.bed b/tests/test_files/test.bed
new file mode 100644
index 0000000..b75f352
--- /dev/null
+++ b/tests/test_files/test.bed
@@ -0,0 +1 @@
+9 94175956 94176036 hsa-let-7a-1 0 +
diff --git a/tests/test_files/test.gff b/tests/test_files/test.gff
new file mode 100644
index 0000000..00e05f0
--- /dev/null
+++ b/tests/test_files/test.gff
@@ -0,0 +1,3 @@
+9 . miRNA_primary_transcript 94175957 94176036 . + . ID=MI0000060;Alias=MI0000060;Name=hsa-let-7a-1
+9 . miRNA 94175962 94175983 . + . ID=MIMAT0000062_2;Alias=MIMAT0000062;Name=hsa-let-7a-5p;Derives_from=MI0000060
+9 . miRNA 94176013 94176033 . + . ID=MIMAT0004481_1;Alias=MIMAT0004481;Name=hsa-let-7a-3p;Derives_from=MI0000060
--
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