samtools.view,mosdepth.depth: add targets parameter

2 files changed, 91 insertions, 40 deletions

diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 2a72989..4627071 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,21 +1,36 @@
-{ bionix
-, indexAttrs ? { }
-, flags ? null
+{
+  bionix,
+  indexAttrs ? {},
+  targets ? null,
+  flags ? null,
 }:
-
 with bionix;
 with lib;
-
-input:
-
-stage {
-  name = "mosdepth-depth";
-  buildInputs = with pkgs; [ mosdepth ];
-  buildCommand = ''
-    mkdir $out
-    ln -s ${input} input.bam
-    ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
-    mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
-  '';
-  passthru.multicore = true;
-}
+  input: let
+    handleTarget = x: let
+      type = builtins.typeOf x;
+      handler = handlers."${type}" or (builtins.throw "mosdepth-depth:unhandled target type:${type}");
+      handlers = {
+        string = handleTarget [x];
+        list = let
+          file = pkgs.writeText "target.bed" (concatStringsSep "\n" x);
+        in "-b ${file}";
+        path = "-b ${x}";
+        set = "-b ${x}";
+      };
+    in
+      handler;
+  in
+    stage {
+      name = "mosdepth-depth";
+      buildInputs = with pkgs; [mosdepth];
+      buildCommand = ''
+        mkdir $out
+        ln -s ${input} input.bam
+        ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
+        mosdepth -t $NIX_BUILD_CORES \
+          ${optionalString (targets != null) (handleTarget targets)} \
+          ${optionalString (flags != null) flags} $out/out input.bam
+      '';
+      passthru.multicore = true;
+    }
diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix
index 4d2bdc7..4966b13 100644
--- a/tools/samtools-view.nix
+++ b/tools/samtools-view.nix
@@ -1,27 +1,63 @@
-{ bionix
-, nameSort ? false
-, flags ? null
-, outfmt ? null
-}:
-
-input:
-
+{
+  bionix,
+  nameSort ? false,
+  flags ? null,
+  outfmt ? null,
+  targets ? null,
+}: input:
 with bionix;
 with lib;
 with types;
+assert (matchFiletype "samtools-view" {
+    bam = _: true;
+    sam = _: true;
+    cram = _: true;
+  }
+  input); let
+  handleTarget = x: let
+    type = builtins.typeOf x;
+    handler = handlers."${type}" or (builtins.throw "samtools-view:unhandled target type:${type}");
+    handlers = {
+      string = handleTarget [x];
+      list = let
+        file = pkgs.writeText "target.bed" (concatStringsSep "\n" x);
+      in "--target-file ${file}";
+      path = "--target-file ${x}";
+      set = "--target-file ${x}";
+    };
+  in
+    handler;
 
-assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: true; } input);
-
-let
-  outfmtR = if outfmt != null then (if builtins.typeOf outfmt == "string" then { "bam" = toBam; "cram" = toCram; "sam" = toSam; }."${outfmt}" else outfmt) input else input.filetype;
-  fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref;
-  outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } { filetype = outfmtR; };
+  outfmtR =
+    if outfmt != null
+    then
+      (
+        if builtins.typeOf outfmt == "string"
+        then
+          {
+            "bam" = toBam;
+            "cram" = toCram;
+            "sam" = toSam;
+          }
+          ."${outfmt}"
+        else outfmt
+      )
+      input
+    else input.filetype;
+  fa = ref: matchFiletype "samtools-view-ref" {fa = _: ref;} ref;
+  outfmtFlags = matchFiletype "samtools-view-outfmt" {
+    bam = _: "-O BAM";
+    sam = _: "-O SAM";
+    cram = x: "-O CRAM -T ${fa x.ref}";
+  } {filetype = outfmtR;};
 in
-stage {
-  name = "samtools-view";
-  buildInputs = with pkgs; [ samtools ];
-  buildCommand = ''
-    samtools view ${outfmtFlags} ${optionalString (flags != null) flags} ${input} > $out
-  '';
-  passthru.filetype = outfmtR;
-}
+  stage {
+    name = "samtools-view";
+    buildInputs = with pkgs; [samtools];
+    buildCommand = ''
+      samtools view \
+        ${optionalString (targets != null) (handleTarget targets)} \
+        ${outfmtFlags} ${optionalString (flags != null) flags} ${input} > $out
+    '';
+    passthru.filetype = outfmtR;
+  }