Temp fixes in pre_imputation_check

Author: aleksandr-medvedev-msc

rules/relatives_ibis.smk

@@ -96,7 +96,7 @@ rule ersa:
         TEMPFILE=ersa/temp_relatives.tsv
         rm -f $TEMPFILE
         rm -f {output}
-
+        echo "ersa --avuncular-adj -ci -a {params.a} --dmax 14 -t {params.t} -l {params.l} {params.r} -th {params.th}"
         for input_file in $FILES; do
             ersa --avuncular-adj -ci -a {params.a} --dmax 14 -t {params.t} -l {params.l} \
                 {params.r} -th {params.th} $input_file -o $TEMPFILE |& tee {log}

scripts/client_background_test.py

@@ -52,7 +52,7 @@ def extract_cb_matches_from_local(input150_path: str, input18_path: str, local_m
 if __name__ == '__main__':
     input150_samples_path = 'workdir/input150.samples'    
     input18_samples_path = 'workdir/input18.samples'
-    local_matches_path = 'workdir/relatives_ibis168.tsv'
+    local_matches_path = 'workdir/relatives_ibis168_3.tsv'
     cb_matches_path = 'workdir/relatives_cb_input18_150_2.tsv'
 
     local_cb_matches_path = 'workdir/relatives_18_150_2.tsv'

scripts/pre_imputation_check.py

@@ -120,6 +120,8 @@ def pre_imputation_check(params, reference):
                     elif matching == 3:
                         flip_file.write(id_ + "\n")
                         flip_swap += 1
+            else:
+                print(id_)
 
     logging.info("Exclude: {} Keep: {}".format(exclude, in_ref - exclude))
     logging.info("Total flip: {}.".format(strand_flip))