From da0384505ac2eda2ee91018323411988012396e5 Mon Sep 17 00:00:00 2001 From: rnmitchell Date: Wed, 23 Apr 2025 05:41:46 -0400 Subject: [PATCH 1/2] fixed bug in GUI --- lusSTR/cli/gui.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lusSTR/cli/gui.py b/lusSTR/cli/gui.py index e2fc94b0..65d914fc 100644 --- a/lusSTR/cli/gui.py +++ b/lusSTR/cli/gui.py @@ -922,8 +922,8 @@ def show_SNP_page(): clicked_wd = col1.button("Please Select An Output Folder") if clicked_wd: - wd = folder_picker_dialog() - st.session_state.wd_dirname = wd + wd_dirname = folder_picker_dialog() + st.session_state.wd_dirname = wd_dirname # Display selected path if st.session_state.wd_dirname: @@ -937,7 +937,7 @@ def show_SNP_page(): if st.button("Submit"): # Check if all required fields are filled - if analysis_software and samp_input and output and wd_dirname: + if analysis_software and samp_input and output and st.session_state.wd_dirname: # Validate output prefix if not validate_prefix(output): @@ -976,7 +976,7 @@ def show_SNP_page(): command = ["lusstr", "snps", "all"] # Specify WD to lusSTR - if wd_dirname: + if st.session_state.wd_dirname: command.extend(["-w", st.session_state.wd_dirname + "/"]) # Run lusSTR command in terminal From b28636c6610c31acf5491c01291692b76d3c9383 Mon Sep 17 00:00:00 2001 From: rnmitchell Date: Wed, 23 Apr 2025 12:39:24 -0400 Subject: [PATCH 2/2] added detection threshold of 10 --- lusSTR/wrappers/snps_convert.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lusSTR/wrappers/snps_convert.py b/lusSTR/wrappers/snps_convert.py index ad732760..82f91a29 100644 --- a/lusSTR/wrappers/snps_convert.py +++ b/lusSTR/wrappers/snps_convert.py @@ -158,7 +158,7 @@ def straitrazor_filtering(sr_df, thresh): if sr_df.loc[i, "Issues"] == "Allele call does not match expected allele!": sr_df = sr_df.drop(i) else: - if allele_reads < (total_snp_reads * thresh): + if allele_reads < (total_snp_reads * thresh) or allele_reads < 11: sr_df.loc[i, "Reads"] = 0 return sr_df