From 81cfa50e6b345942951b68eac0e184ea025f2ae4 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 23 Aug 2022 18:36:40 +1000
Subject: last: align only a single fastq file

---
 test-tnpair.nix      | 2 +-
 tools/last-align.nix | 8 +++-----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 169d531..195ac27 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -60,7 +60,7 @@ let
   alignments = {
     "bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
     "subread.bam" = subread.align { inherit ref; } tnpair.normal.files;
-    "last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
+    "last.maf" = lastal.align { inherit ref; } tnpair.normal.files.input1;
     "whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
     "bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
     "bwa-mem2.bam" = bwa.mem2 { inherit ref; } tnpair.normal.files;
diff --git a/tools/last-align.nix b/tools/last-align.nix
index fbc0914..0643419 100644
--- a/tools/last-align.nix
+++ b/tools/last-align.nix
@@ -5,9 +5,7 @@
 , indexAttrs ? { }
 }:
 
-{ input1
-, input2 ? null
-}:
+input:
 
 with bionix;
 with lib;
@@ -23,13 +21,13 @@ stage {
       last-train -P $NIX_BUILD_CORES \
         ${optionalString (trainFlags != null) flags} \
         ${bionix.lastal.index indexAttrs ref}/index \
-        ${fq input1} ${optionalString (input2 != null) (fq input2)}\
+        ${fq input} -Q 1\
         > train
       lastal -P $NIX_BUILD_CORES \
         ${optionalString (flags != null) flags} \
         ${bionix.lastal.index indexAttrs ref}/index \
         -p train \
-        ${fq input1} ${optionalString (input2 != null) (fq input2)}\
+        ${fq input} -Q 1 \
         > tmp
     cp tmp $out
  '';
-- 
cgit v1.2.3