diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 444319b..d88013a 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -55,7 +55,7 @@ Output Arguments Peeling output options: - -no_dosages Flag to suppress the dosage files. + -no_dosage Flag to suppress the dosage files. -no_seg Flag to suppress the segregation files (e.g. when running for chip imputation and not hybrid peeling). -no_params Flag to suppress writing the parameter files. @@ -67,7 +67,7 @@ Output Arguments -binary_call_files Flag to write out the called genotype files as a binary plink output [Not yet implemented]. -By default |Software| produces a dosages file, a segregation files and two parameter files (genotyping error and recombination rate). Creation of these files can be suppressed with the ``-no_dosages``, ``-no_seg``, and ``-no_params`` options. |Software| can also write out the genotype probability file (.haps) with the `-haps` argument. +By default |Software| produces a dosage file, a segregation files and two parameter files (genotyping error and recombination rate). Creation of these files can be suppressed with the ``-no_dosages``, ``-no_seg``, and ``-no_params`` options. |Software| can also write out the genotype probability file (.haps) with the `-haps` argument. The ``-calling_threshold`` arguments controls which genotypes (and phased haplotypes) are called as part of the algorithm. A calling threshold of 0.9 indicates that genotypes are only called if greater than 90% of the final probability mass is on that genotype. Using a higher-value will increase the accuracy of called genotypes, but will result in fewer genotypes being called. Since there are three genotypes states, "best-guess" genotypes are produced with a calling threshold less than ``0.33``. ``-calling_threshThe ``-binary_call_files`` option can be used to change the output to a plink binary format. diff --git a/src/tinypeel/tinypeel.py b/src/tinypeel/tinypeel.py index 58cbd15..efd080f 100644 --- a/src/tinypeel/tinypeel.py +++ b/src/tinypeel/tinypeel.py @@ -255,7 +255,7 @@ def getArgs(): "-no_dosage", action="store_true", required=False, - help="Flag to suppress the dosage files.", + help="Flag to suppress the output of the dosage file.", ) output_parser.add_argument( "-no_seg", diff --git a/tests/functional_tests/runTests.sh b/tests/functional_tests/runTests.sh index dc6fdb0..157a27f 100755 --- a/tests/functional_tests/runTests.sh +++ b/tests/functional_tests/runTests.sh @@ -237,7 +237,7 @@ $tinypeel -genotypes test7c/genotypes.txt \ -out test7c/outputs/output Rscript checkResults.r 7c -# Test 8: Check to make sure the no_dosages, no_seg, no_params flags work, and the haps file works. +# Test 8: Check to make sure the no_dosage, no_seg, no_params flags work, and the haps file works. rm -rf test8/outputs mkdir test8/outputs @@ -248,8 +248,8 @@ $tinypeel -genotypes test8/genotypes.txt \ -seqfile test8/seqfile.txt \ -pedigree test8/pedigree.txt \ -runType multi \ - -no_dosages \ - -out test8/outputs/no_dosages + -no_dosage \ + -out test8/outputs/no_dosage $tinypeel -genotypes test8/genotypes.txt \ -phasefile test8/phasefile.txt \ -penetrance test8/penetrance.txt \