Merge pull request #21 from bcgsc/lai_gzip

Fix --lai mode to work with gzipped reference files

Author: warrenlr

ntRootAncestryPredictor.pl

@@ -234,6 +234,11 @@ sub usage_page {
 if ($verbose) {
 	print "\n\tnz: Non-zero\n";
 }
-print "\n\nAncestry predictions available in:\n$out\n\n";
+print "\n\nAncestry predictions available in:\n$out\n";
+
+if ($tile_resolution) {
+	print $f . "_ancestry-predictions-tile-resolution_tile$dw.tsv\n";
+}
+print "\n";
 
 exit(0);

ntroot_run_pipeline.smk

@@ -100,8 +100,11 @@ rule samtools_faidx:
     output: out_fai = f"{draft_base}.fai"
     params:
         benchmark = f"{time_command} samtools_faidx_{draft_base}.time"
-    shell:
-        "{params.benchmark} samtools faidx -o {output.out_fai} {input.reference}"
+    run:
+        if input.reference.endswith(".gz"):
+            shell("{params.benchmark} gunzip -c {input.reference} |samtools faidx -o {output.out_fai} -")
+        else:
+            shell("{params.benchmark} samtools faidx -o {output.out_fai} {input.reference}")
 
 rule ancestry_prediction:
     input: