diff --git a/somalier.nimble b/somalier.nimble index 3d6aff8..e16624c 100644 --- 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 index 3eed818..cd72acb 100644 --- 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 index c36d91d..8541525 100644 --- a/src/somalierpkg/version.nim +++ b/src/somalierpkg/version.nim @@ -1 +1 @@ -let somalierVersion* = "0.2.14" +let somalierVersion* = "0.2.15"