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|
{ 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"; name = _: "name"; } x;};}) inputs)) == 1;
nameSorted = matchFiletype "samtools-merge" { bam = x: matchSorting "samtools-merge" {coord = _: false; name = _: true;} x;} (lib.head inputs);
in
assert inputIsHomogenous;
if length inputs == 1 then head inputs else
stage {
name = "samtools-merge";
buildInputs = with pkgs; [ samtools ];
buildCommand = ''
samtools merge ${optionalString (flags != null) flags} \
${if nameSorted then "-n" else ""} \
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;
}
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