changed no_dosages to no_dosage #90

AlphaGenes · Oct 9, 2023 · df917e1 · df917e1
1 parent 7586308
commit df917e1
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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 \