Modify EvidenceQC to not create/expect additional column in median co…

…verage file (#745) * Modified python scripts to not create/expect additional column * Removed iloc call
broadinstitute · Nov 15, 2024 · c120767 · c120767
1 parent 9f8e93e
commit c120767
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diff --git a/src/WGD/bin/medianCoverage.R b/src/WGD/bin/medianCoverage.R
@@ -122,6 +122,6 @@ if(opts$binwise==TRUE){
   write.table(res,args$args[2], sep="\t", col.names=T, row.names=F, quote=F)
 }else{
   res <- covPerSample(cov,mad=opts$mad)
-  names(res)[1] <- "sample_id"
+  names(res)[1] <- "#sample_id"
   write.table(res,args$args[2], sep="\t", col.names=T, row.names=F, quote=F)
 }
diff --git a/src/sv-pipeline/scripts/make_evidence_qc_table.py b/src/sv-pipeline/scripts/make_evidence_qc_table.py
@@ -51,7 +51,7 @@ def read_bincov_median(filename: str) -> pd.DataFrame:
     df_median = pd.read_csv(filename, sep="\t").T
     df_median = df_median.rename_axis(ID_COL).reset_index()
     df_median.columns = [ID_COL, "median_coverage"]
-    df_median = df_median.iloc[1:].reset_index(drop=True)
+    df_median = df_median.reset_index(drop=True)
     return df_median