diff options
| author | Justin Bedo <cu@cua0.org> | 2019-05-02 07:45:02 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-05-02 07:45:02 +1000 |
| commit | e7a2705bb3818db7647c7a37ef675760c323bd26 (patch) | |
| tree | bfab0205d6414f8ee0c76c80c5bc21866e310db6 | |
| parent | 95c8a36a7e673fac090175729069a668daa919da (diff) | |
samtools-merge: detect correct sorting
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/samtools-merge.nix | 7 |
2 files changed, 7 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 1b5f347..f2e84ac 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -13,6 +13,7 @@ let alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; sort = samtools.sort {}; + nameSort = samtools.sort {nameSort = true;}; flagstat = samtools.flagstat {}; check-fastqc = fastqc.check {}; check-fastp = fastp.run {}; @@ -56,6 +57,7 @@ let (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2") (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3") (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam") + (ln (samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)]) "alignments/merged-namesorted.bam") (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram") #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram") (ln (flagstat tnpairResult.alignments.tumour) "alignments/${tnpair.tumour.name}.flagstat") diff --git a/tools/samtools-merge.nix b/tools/samtools-merge.nix index 9b7d133..81b0c15 100644 --- a/tools/samtools-merge.nix +++ b/tools/samtools-merge.nix @@ -10,7 +10,8 @@ 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; + 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; @@ -19,7 +20,9 @@ stage { name = "samtools-merge"; buildInputs = with pkgs; [ samtools ]; buildCommand = '' - samtools merge ${optionalString (flags != null) flags} out.bam ${concatStringsSep " " inputs} + 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 |