fix empty bam bug in m3c contact call

Author: lhqing

cemba_data/hisat3n/hisat3n_m3c.py

@@ -635,14 +635,18 @@ def _dedup_contacts(output_prefix, save_raw=False):
     total_dedup = []
     for _, chrom_df in contacts.groupby(['chrom1', 'chrom2']):
         total_dedup.append(_dedup_chrom_df(chrom_df))
-    total_dedup = pd.concat(total_dedup)
+    try:
+        total_dedup = pd.concat(total_dedup)
+    except ValueError:
+        # no dataframes in total_dedup
+        total_dedup = pd.DataFrame(columns=contacts.columns)
     total_dedup.to_csv(output_path, sep='\t', index=False)
 
     if not save_raw:
         subprocess.run(shlex.split(f'rm -f {input_path}'), check=True)
 
     dedup_contacts = total_dedup.shape[0]
-    dup_rate = (input_contacts - dedup_contacts) / input_contacts
+    dup_rate = (input_contacts - dedup_contacts) / (input_contacts + 0.00001)
     return dedup_contacts, dup_rate
 
 

hisat3n_env.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
- - python=3.8
+ - python=3.9
  - pip
  - jupyter
  - snakemake
@@ -15,12 +15,10 @@ dependencies:
  - samtools
  - picard
  - bedtools
- - htslib>=1.9
+ - htslib=1.15
  - pysam
  - pybedtools
  - pyBigWig
- - star=2.7.3a
- - subread=2.0
  - pip:
     - papermill
     - allcools