fix for hts-nim bug

brentp · Jan 11, 2022 · 5d7a5d8 · 5d7a5d8
1 parent 6a720c7
commit 5d7a5d8
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/somalier.nimble b/somalier.nimble
@@ -1,6 +1,6 @@
 #import somalierpkg/version as _
 
-version       = "0.2.14" #somalierVersion
+version       = "0.2.15" #somalierVersion
 author        = "Brent Pedersen"
 description   = "sample-swap checking directly on BAMs/CRAMs for cancer data"
 license       = "academic only"
@@ -10,7 +10,7 @@ license       = "academic only"
 # Dependencies
 
 requires "https://github.com/brentp/zip#dev"
-requires "nim >= 1.2.0", "hts >= 0.3.17", "https://github.com/brentp/pedfile >= 0.0.3", "https://github.com/brentp/hileup", "argparse == 0.10.1", "lapper", "arraymancer#head"
+requires "nim >= 1.2.0", "hts >= 0.3.20", "https://github.com/brentp/pedfile >= 0.0.3", "https://github.com/brentp/hileup", "argparse == 0.10.1", "lapper", "arraymancer#head"
 requires "https://github.com/brentp/slivar#head"
 srcDir = "src"
 

diff --git a/src/somalierpkg/findsites.nim b/src/somalierpkg/findsites.nim
@@ -22,6 +22,7 @@ type vf = object
 var target_af = 0.48
 if getEnv("SOMALIER_TARGET_AF") != "":
     target_af = parseFloat(getEnv("SOMALIER_TARGET_AF"))
+    stderr.write_line &"[somalier/find-sites] using {target_af:.2f} as the target allele frequency"
 
 proc vf_by(a:vf, b:vf): int =
   return cmp((a.af - target_af).abs, (b.af - target_af).abs)
@@ -114,7 +115,7 @@ proc findsites_main*() =
 
   if not open(vcf, opts.vcf, threads=2):
     quit "couldn't open " & opts.vcf
-  vcf.set_samples(@[])
+  vcf.set_samples(@["^"])
   var out_path = "sites.vcf.gz"
   if not open(wtr, out_path, mode="wz", threads=1):
     quit "couldn't open stdout for writing sites"

diff --git a/src/somalierpkg/version.nim b/src/somalierpkg/version.nim
@@ -1 +1 @@
-let somalierVersion* = "0.2.14"
+let somalierVersion* = "0.2.15"