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@tgaspe
tgaspe committed Aug 28, 2024
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310 changes: 93 additions & 217 deletions src/bcftools/bcftools_annotate/test.sh
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name: bcftools_stats
namespace: bcftools
description: |
Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats.
When two files are given, the program generates separate stats for intersection
and the complements. By default only sites are compared, -s/-S must given to include
also sample columns.
keywords: [Stats, VCF, BCF]
links:
homepage: https://samtools.github.io/bcftools/
documentation: https://samtools.github.io/bcftools/bcftools.html#stats
repository: https://github.com/samtools/bcftools
issue_tracker: https://github.com/samtools/bcftools/issues
references:
doi: https://doi.org/10.1093/gigascience/giab008
license: MIT/Expat, GNU
requirements:
commands: [bcftools]
authors:
- __merge__: /src/_authors/theodoro_gasperin.yaml
roles: [ author, maintainer ]

argument_groups:
- name: Inputs
arguments:
- name: --input
alternatives: -i
type: file
multiple: true
description: Input VCF/BCF file. Maximum of two files.
required: true

- name: Outputs
arguments:
- name: --output
alternatives: -o
direction: output
type: file
description: Output txt statistics file.
required: true

- name: Options
arguments:

- name: --allele_frequency_bins
alternatives: --af_bins
type: string
description: |
Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\n0.5\n1).

- name: --allele_frequency_tag
alternatives: --af_tag
type: string
description: |
Allele frequency tag to use, by default estimated from AN,AC or GT.

- name: --first_allele_only
alternatives: --first_only
type: boolean_true
description: |
Include only 1st allele at multiallelic sites

- name: --collapse
alternatives: --c
type: string
choices: [ snps, indels, both, all, some, none ]
description: |
Treat as identical records with <snps|indels|both|all|some|none>.
See https://samtools.github.io/bcftools/bcftools.html#common_options for details.

- name: --depth
alternatives: --d
type: string
description: |
Depth distribution: min,max,bin size [0,500,1]
example: 0,500,1

- name: --exclude
alternatives: --e
type: string
description: |
Exclude sites for which the expression is true.
See https://samtools.github.io/bcftools/bcftools.html#expressions for details.

- name: --exons
alternatives: --E
type: file
description: |
tab-delimited file with exons for indel frameshifts statistics.
The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions.
The file is BGZF-compressed and indexed with tabix
e.g.
tabix -s1 -b2 -e3 file.gz

- name: --apply_filters
alternatives: --f
type: string
description: |
Require at least one of the listed FILTER strings (e.g. "PASS,.")

- name: --fasta_reference
alternatives: --F
type: file
description: |
Faidx indexed reference sequence file to determine INDEL context

- name: --include
alternatives: --i
type: string
description: |
Select sites for which the expression is true.
See https://samtools.github.io/bcftools/bcftools.html#expressions for details.

- name: --split_by_ID
alternatives: --I
type: boolean_true
description: |
Collect stats for sites with ID separately (known vs novel)

- name: --regions
alternatives: --r
type: string
description: |
Restrict to comma-separated list of regions

- name: --regions_file
alternatives: --R
type: file
description: |
Restrict to regions listed in a file.

- name: --regions_overlap
type: string
choices: ['pos', 'record', 'variant', '0', '1', '2']
description: |
This option controls how overlapping records are determined:
set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T);
set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R,
and includes indels with POS at the end of a region, which are technically outside the region);
or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-").

- name: --samples
alternatives: --s
type: string
description: |
List of samples for sample stats, "-" to include all samples.

- name: --samples_file
alternatives: --S
type: file
description: |
File of samples to include.

- name: --targets
alternatives: --t
type: string
description: |
Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF
rather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the
index to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets
can be prefixed with "^" to request logical complement. For example, "^X,Y,MT" indicates that
sequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is
that -r/-R checks for proper overlaps and considers both POS and the end position of an indel,
while -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap).
Note that -t cannot be used in combination with -T.

- name: --targets_file
alternatives: --T
type: file
description: |
Similar to -R but streams rather than index-jumps.

- name: --targets_overlaps
type: string
choices: ['pos', 'record', 'variant', '0', '1', '2']
description: |
Include if POS in the region (0), record overlaps (1), variant overlaps (2).

- name: --user_tstv
alternatives: --u
type: string
description: |
Collect Ts/Tv stats for any tag using the given binning [0:1:100].
A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag.

- name: --verbose
alternatives: --v
type: boolean_true
description: |
Produce verbose per-site and per-sample output.

resources:
- type: bash_script
path: script.sh

test_resources:
- type: bash_script
path: test.sh

engines:
- type: docker
image: debian:stable-slim
setup:
- type: apt
packages: [bcftools, procps]
- type: docker
run: |
echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt
test_setup:
- type: apt
packages: [tabix]

runners:
- type: executable
- type: nextflow


#!/bin/bash

## VIASH START
## VIASH END

# Exit on error
set -eo pipefail

#test_data="$meta_resources_dir/test_data"

#############################################
# helper functions
assert_file_exists() {
[ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
}
assert_file_not_empty() {
[ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
}
assert_file_contains() {
grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
}
assert_identical_content() {
diff -a "$2" "$1" \
|| (echo "Files are not identical!" && exit 1)
}
#############################################

# Create directories for tests
echo "Creating Test Data..."
TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
function clean_up {
[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
}
trap clean_up EXIT

# Create test data
cat <<EOF > "$TMPDIR/example.vcf"
##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##contig=<ID=19,length=58617616>
##contig=<ID=20,length=58617616>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3
20 1235237 . T . . . . GT 0/0 0|0 ./.
EOF



# Test 1: Default Use
mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null

echo "> Run bcftools_stats on VCF file"
"$meta_executable" \
--input "../example.vcf" \
--output "stats.txt" \

# checks
assert_file_exists "stats.txt"
assert_file_not_empty "stats.txt"
assert_file_contains "stats.txt" "bcftools stats ../example.vcf"
echo "- test1 succeeded -"

popd > /dev/null



echo "---- All tests succeeded! ----"
exit 0

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