blob: 9b7d133c209452d8e5ad27639b96989643e65345 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
{ bionix
, flags ? null
, outfmt ? null
}:
inputs:
with bionix;
with lib;
let
inherit (bionix.types) matchFiletype matchSorting;
inputIsHomogenous = length (unique (map (matchFiletype "samtools-merge" {bam = x: x // {sorting = matchSorting "samtools-merge" {coord = _: "coord";} x;};}) inputs)) == 1;
in
assert inputIsHomogenous;
stage {
name = "samtools-merge";
buildInputs = with pkgs; [ samtools ];
buildCommand = ''
samtools merge ${optionalString (flags != null) flags} out.bam ${concatStringsSep " " inputs}
# Merge is non-deterministic with PG lines; if files have clashing PG IDs then a random
# suffix is appended to make it unique. PG lines are stripped in the following to
# resolve the issue.
samtools reheader <(samtools view -H out.bam | grep -v '@PG') out.bam > $out
'';
passthru.filetype = (builtins.elemAt inputs 0).filetype;
}
|
