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Commit 00c2db18 authored by Alex Kanitz's avatar Alex Kanitz
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test: include reference file

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README.md
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− 37
View file @ 00c2db18
......@@ -27,46 +27,49 @@ prebuilt Docker image from
## Input files
* [BED](https://www.ensembl.org/info/website/upload/bed.html) file
* [BAM](https://samtools.github.io/hts-specs/) file(s)
* Optional: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file compressed
with [`bgzip`](http://www.htslib.org/doc/bgzip.html)
* Optional:
[GFF/GTF/GFF3](https://en.wikipedia.org/wiki/General_feature_format) file
* [BED][bed] file; the score column is ignored, so it can contain arbitrary
values
* [BAM][bam] file(s)
* Optional: [FASTA][fasta] file compressed with [`bgzip`][bgzip]
* Optional: [GFF/GTF/GFF3][gff] file
You can have a look at the test input files in `tests/test_files` to see
examples for each file type. For reference, also the uncompressed counterparts
of BAM and FASTA files (`test.sam` and `test.fa`, respectively) are provided.
## Output files
* Custom file format:
* Custom file format. Output from the provided [Example](#example).
```console
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> hsa-let-7a-1
.....>>>>>>>>>>>>>>>>>>>>>>..................................................... hsa-let-7a-5p
........................................................>>>>>>>>>>>>>>>>>>>>>... hsa-let-7a-3p
TGGGATGAGGTAGTAGGTTGTATAGTTTTAGGGTCACACCCACCACTGGGAGATAACTATACAATCTACTGTCTTTCCTA 9:94175957-94176036:+
TACCATGAGGTAGTAGGTTGTATAGTT..................................................... 1
...CATGAGGTAGTAGGTTGTATAGTT..................................................... 10
...GA-GAGGTAGTAGGTTGTATAGTT..................................................... 2
....A-GAGGTAGTAGGTTGTATAGTT..................................................... 19
.....TGAGGTAGTAGGTTGTATAGTT..................................................... 17
......GAGGTAGTAGGTTGTATAGTT..................................................... 33
.......AGGTAGTAGGTTGTATAGTT..................................................... 9
.......AGGTAGTAGGTTGTATAGTTT.................................................... 2
........GGTAGTAGGTTGTATAGTT..................................................... 7
...................................................GATAACTATACAATCTACTGTCTT..... 1
......................................................AACTATACAATCTACT.......... 1
........................................................CTATACAATCTACTGTCTTTCT.. 28
........................................................CTATACAATCTACTGTCTTTC-T. 22
........................................................CTATACAATCTACTGTCTTTCC.. 19
........................................................CTATACAATCTACTGTCTTTC... 12
........................................................CTATACAATCTACTGTCTTTCTT. 2
........................................................CTATACAATCTACTGTC....... 1
........................................................CTATACAATCTACTGTCTT..... 1
........................................................CTATACAATCTACTGTCTTTCG.. 1
.........................................................TATACAATCTACTGTCTTTCT.. 4
.........................................................TATACAATCTACTGTCTTTC-T. 4
.........................................................TATACAATCTACTGTCTTTC... 2
.........................................................TATACAATCTACTGTCTTTCC.. 1
.........................................................TATACAATCTACTGTCTTTCCT. 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> test-mir
....>>>>>>>>>>>>>>>>>>>>>>..................................................... test-mir-5p
.......................................................>>>>>>>>>>>>>>>>>>>>>... test-mir-3p
ATCTCAGCACTTTGAGAGGCCAAAGTGGATGGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACAAGGTGAA test_ref:3618-3696:+
ACCATGAGGTAGTAGGTTGTATAGTT..................................................... 1
..CATGAGGTAGTAGGTTGTATAGTT..................................................... 10
..GA-GAGGTAGTAGGTTGTATAGTT..................................................... 2
...A-GAGGTAGTAGGTTGTATAGTT..................................................... 19
....TGAGGTAGTAGGTTGTATAGTT..................................................... 17
.....GAGGTAGTAGGTTGTATAGTT..................................................... 33
......AGGTAGTAGGTTGTATAGTT..................................................... 9
......AGGTAGTAGGTTGTATAGTTT.................................................... 2
.......GGTAGTAGGTTGTATAGTT..................................................... 7
..................................................GATAACTATACAATCTACTGTCTT..... 1
.....................................................AACTATACAATCTACT.......... 1
.......................................................CTATACAATCTACTGTCTTTCT.. 28
.......................................................CTATACAATCTACTGTCTTTC-T. 22
.......................................................CTATACAATCTACTGTCTTTCC.. 19
.......................................................CTATACAATCTACTGTCTTTC... 12
.......................................................CTATACAATCTACTGTCTTTCTT. 2
.......................................................CTATACAATCTACTGTC....... 1
.......................................................CTATACAATCTACTGTCTT..... 1
.......................................................CTATACAATCTACTGTCTTTCG.. 1
........................................................TATACAATCTACTGTCTTTCT.. 4
........................................................TATACAATCTACTGTCTTTC-T. 4
........................................................TATACAATCTACTGTCTTTC... 2
........................................................TATACAATCTACTGTCTTTCC.. 1
........................................................TATACAATCTACTGTCTTTCCT. 1
```
## Example
......@@ -78,6 +81,7 @@ available, you can use the following command to run a test:
```bash
ascii_alignment_pileup.R \
--verbose \
--reference="tests/test_files/test.fa.gz" \
--annotations="tests/test_files/test.gff" \
--output-directory="$PWD" \
"tests/test_files/test.bed" \
......@@ -95,8 +99,9 @@ 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.
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`.
## Options
......@@ -149,8 +154,56 @@ In both cases, a successful test will create a file
Print log messages to STDOUT.
```
## Creating a BGZIP-compressed reference
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.
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
with the following command:
```bash
bgzip < test.fa > test.fa.gz
```
To remove the uncompressed file instead, keeping only the compressed copy, do:
```bash
bgzip test.fa
```
Instead of installing HTSlib, you can also use a prebuilt Docker image, e.g.,
from [BioContainers][biocontainers] to create your BGZIP-compressed copy.
For example, when using container image
`quay.io/biocontainers/htslib:1.15.1--h9753748_0`, and again assuming that you
want to compress file `test.fa` in your current working directory, you can
create and run the following command:
```bash
docker run \
--rm \
-it \
-v $PWD:/data \
quay.io/biocontainers/htslib:1.15.1--h9753748_0 \
bash -c 'bgzip < /data/test.fa > /data/test.fa.gz'
```
You can find other BioContainers-built HTSlib Docker images at:
<https://quay.io/repository/biocontainers/htslib?tab=tags>
## Contact
Email: <zavolab-biozentrum@unibas.ch>
&copy; 2019 Zavolab, Biozentrum, University of Basel
[bam]: <https://samtools.github.io/hts-specs/>
[bed]: <https://www.ensembl.org/info/website/upload/bed.html>
[bgzip]: <http://www.htslib.org/doc/bgzip.html>
[biocontainers]: <https://biocontainers.pro/>
[fasta]: <https://en.wikipedia.org/wiki/FASTA_format>
[gff]: <https://en.wikipedia.org/wiki/General_feature_format>
[htslib]: <https://github.com/samtools/htslib>
\ No newline at end of file
tests/test_files/test.bam
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tests/test_files/test.bam.bai
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tests/test_files/test.bed
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9 94175956 94176036 hsa-let-7a-1 0 +
test_ref 3617 3696 test-mir 0 +
tests/test_files/test.fa 0 → 100644
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tests/test_files/test.gff
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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
test_ref . miRNA_primary_transcript 3617 3696 . + . ID=MI0000001;Name=test-mir
test_ref . miRNA 3622 3643 . + . ID=MIMAT0000062_2;Name=test-mir-5p;Derives_from=MI0000001
test_ref . miRNA 3673 3693 . + . ID=MIMAT0004481_1;Name=test-mir-3p;Derives_from=MI0000001
tests/test_files/test.sam 0 → 100644
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@HD VN:1.0 SO:coordinate
@SQ SN:test_ref LN:60000
560307.1 0 test_ref 3614 255 3M1I27M * 0 0 CTGCTACCATGAGGTAGTAGGTTGTATAGTT *
47809.1 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.2 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.3 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.4 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.5 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.6 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.7 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
47809.8 0 test_ref 3620 255 24M * 0 0 CATGAGGTAGTAGGTTGTATAGTT *
137814.1 0 test_ref 3620 255 1M1I23M * 0 0 CCATGAGGTAGTAGGTTGTATAGTT *
137814.2 0 test_ref 3620 255 1M1I23M * 0 0 CCATGAGGTAGTAGGTTGTATAGTT *
184691.1 0 test_ref 3620 255 2M1D21M * 0 0 GAGAGGTAGTAGGTTGTATAGTT *
184691.2 0 test_ref 3620 255 2M1D21M * 0 0 GAGAGGTAGTAGGTTGTATAGTT *
7538.1 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.2 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.3 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.4 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.5 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.6 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.7 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.8 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.9 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.10 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.11 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.12 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.13 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.14 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.15 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.16 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.19 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.20 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
7538.21 0 test_ref 3621 255 1M1D21M * 0 0 AGAGGTAGTAGGTTGTATAGTT *
146.29 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.30 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.31 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.32 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.35 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.36 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.37 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.38 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.39 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.40 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.41 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.42 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.43 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.44 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.45 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.46 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
146.47 0 test_ref 3622 255 22M * 0 0 TGAGGTAGTAGGTTGTATAGTT *
1239.489 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.493 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.494 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.495 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.496 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.497 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.498 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.499 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.500 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.501 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.502 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.503 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.504 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.505 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.506 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.507 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.508 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.509 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.510 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.511 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.512 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.513 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.514 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.515 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.516 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.517 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.518 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.519 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.520 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.521 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.522 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.523 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
1239.524 0 test_ref 3623 255 21M * 0 0 GAGGTAGTAGGTTGTATAGTT *
69912.1 0 test_ref 3624 255 1M2I19M * 0 0 ACAGGTAGTAGGTTGTATAGTT *
69912.2 0 test_ref 3624 255 1M2I19M * 0 0 ACAGGTAGTAGGTTGTATAGTT *
69912.3 0 test_ref 3624 255 1M2I19M * 0 0 ACAGGTAGTAGGTTGTATAGTT *
69912.4 0 test_ref 3624 255 1M2I19M * 0 0 ACAGGTAGTAGGTTGTATAGTT *
69912.5 0 test_ref 3624 255 1M2I19M * 0 0 ACAGGTAGTAGGTTGTATAGTT *
159389.1 0 test_ref 3624 255 20M * 0 0 AGGTAGTAGGTTGTATAGTT *
159389.2 0 test_ref 3624 255 20M * 0 0 AGGTAGTAGGTTGTATAGTT *
160509.1 0 test_ref 3624 255 1M2I20M * 0 0 ACAGGTAGTAGGTTGTATAGTTT *
160509.2 0 test_ref 3624 255 1M2I20M * 0 0 ACAGGTAGTAGGTTGTATAGTTT *
163163.1 0 test_ref 3624 255 1M2I19M * 0 0 AAAGGTAGTAGGTTGTATAGTT *
163163.2 0 test_ref 3624 255 1M2I19M * 0 0 AAAGGTAGTAGGTTGTATAGTT *
18647.1 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.2 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.3 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.4 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.5 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.6 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
18647.7 0 test_ref 3625 255 19M * 0 0 GGTAGTAGGTTGTATAGTT *
654482.1 0 test_ref 3668 255 24M * 0 0 GATAACTATACAATCTACTGTCTT *
700221.1 16 test_ref 3671 255 16M * 0 0 AACTATACAATCTACT *
20198.1 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.2 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.3 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.4 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.5 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.6 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.7 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.8 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.9 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.10 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.11 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.12 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.13 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.14 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.15 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.16 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.17 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.18 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.25 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.26 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.27 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.28 0 test_ref 3673 255 21M1D1M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.1 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.2 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.3 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.4 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.5 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.6 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.7 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.8 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.9 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.10 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.11 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.12 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.13 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.14 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.15 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.16 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.17 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.18 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.19 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.20 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.21 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.22 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.23 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.24 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.25 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.26 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.27 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
20198.28 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCT *
26401.1 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.2 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.3 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.4 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.5 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.6 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.7 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.8 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.9 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.10 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.11 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.12 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.13 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.14 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.15 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.16 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.17 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.18 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
26401.19 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCC *
36169.1 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.2 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.3 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.4 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.5 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.6 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.7 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.8 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.9 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.10 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.11 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
36169.12 0 test_ref 3673 255 21M * 0 0 CTATACAATCTACTGTCTTTC *
171162.1 0 test_ref 3673 255 23M * 0 0 CTATACAATCTACTGTCTTTCTT *
171162.2 0 test_ref 3673 255 23M * 0 0 CTATACAATCTACTGTCTTTCTT *
329376.1 0 test_ref 3673 255 17M * 0 0 CTATACAATCTACTGTC *
582692.1 0 test_ref 3673 255 22M * 0 0 CTATACAATCTACTGTCTTTCG *
767388.1 0 test_ref 3673 255 19M * 0 0 CTATACAATCTACTGTCTT *
83975.1 0 test_ref 3674 255 21M * 0 0 TATACAATCTACTGTCTTTCT *
83975.2 0 test_ref 3674 255 21M * 0 0 TATACAATCTACTGTCTTTCT *
83975.3 0 test_ref 3674 255 21M * 0 0 TATACAATCTACTGTCTTTCT *
83975.4 0 test_ref 3674 255 21M * 0 0 TATACAATCTACTGTCTTTCT *
83975.1 0 test_ref 3674 255 20M1D1M * 0 0 TATACAATCTACTGTCTTTCT *
83975.2 0 test_ref 3674 255 20M1D1M * 0 0 TATACAATCTACTGTCTTTCT *
83975.3 0 test_ref 3674 255 20M1D1M * 0 0 TATACAATCTACTGTCTTTCT *
83975.4 0 test_ref 3674 255 20M1D1M * 0 0 TATACAATCTACTGTCTTTCT *
203160.1 0 test_ref 3674 255 20M * 0 0 TATACAATCTACTGTCTTTC *
203160.2 0 test_ref 3674 255 20M * 0 0 TATACAATCTACTGTCTTTC *
530700.1 0 test_ref 3674 255 21M * 0 0 TATACAATCTACTGTCTTTCC *
728216.1 0 test_ref 3674 255 22M * 0 0 TATACAATCTACTGTCTTTCCT *
tests/test_files/test.test-mir.min.1.pileup.tab 0 → 100644
+ 28
− 0
View file @ 00c2db18
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> test-mir
....>>>>>>>>>>>>>>>>>>>>>>..................................................... test-mir-5p
.......................................................>>>>>>>>>>>>>>>>>>>>>... test-mir-3p
ATCTCAGCACTTTGAGAGGCCAAAGTGGATGGATCACTTGAGGCCAGGAGTTCAAGACCAGCCTGGCCAACAAGGTGAA test_ref:3618-3696:+
ACCATGAGGTAGTAGGTTGTATAGTT..................................................... 1
..CATGAGGTAGTAGGTTGTATAGTT..................................................... 10
..GA-GAGGTAGTAGGTTGTATAGTT..................................................... 2
...A-GAGGTAGTAGGTTGTATAGTT..................................................... 19
....TGAGGTAGTAGGTTGTATAGTT..................................................... 17
.....GAGGTAGTAGGTTGTATAGTT..................................................... 33
......AGGTAGTAGGTTGTATAGTT..................................................... 9
......AGGTAGTAGGTTGTATAGTTT.................................................... 2
.......GGTAGTAGGTTGTATAGTT..................................................... 7
..................................................GATAACTATACAATCTACTGTCTT..... 1
.....................................................AACTATACAATCTACT.......... 1
.......................................................CTATACAATCTACTGTCTTTCT.. 28
.......................................................CTATACAATCTACTGTCTTTC-T. 22
.......................................................CTATACAATCTACTGTCTTTCC.. 19
.......................................................CTATACAATCTACTGTCTTTC... 12
.......................................................CTATACAATCTACTGTCTTTCTT. 2
.......................................................CTATACAATCTACTGTC....... 1
.......................................................CTATACAATCTACTGTCTT..... 1
.......................................................CTATACAATCTACTGTCTTTCG.. 1
........................................................TATACAATCTACTGTCTTTCT.. 4
........................................................TATACAATCTACTGTCTTTC-T. 4
........................................................TATACAATCTACTGTCTTTC... 2
........................................................TATACAATCTACTGTCTTTCC.. 1
........................................................TATACAATCTACTGTCTTTCCT. 1
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