update to 0.5.6:

avoids "AssertionError: fragment start greater
 than fragmentend for read <read name>".
 for reads with template length 0.

CHANGES.txt

@@ -9,4 +9,7 @@ v0.5.3
 v0.5.4
     LIQUORICE_summary now handles samples with numerical names correctly
 v0.5.5
-    Fixes a bug so that now when --save_biasfactor_table is specified, the corrected coverage is saved as well. Adds the --save_corrected_coverage_table flag/parameter.
+    Fixes a bug so that now when --save_biasfactor_table is specified, the corrected coverage is saved as well. Adds the --save_corrected_coverage_table flag/parameter.
+v0.5.6
+    Fixes a bug due to which, when reads with a template length (column 9 in the .bam file) of 0 were provided, in some cases the coverage calculation would fail with the error "AssertionError: fragment start greater than fragmentend for read <read name>".
+    Fragments are now assumed to be not "properly paired" when their insert size length is 0. This may slightly change the results of LIQUORICE in cases were reads with template lengths of 0 were provided.

conda-recipe/meta.yaml

@@ -1,11 +1,12 @@
+{% set version = "0.5.6" %}
+
 package:
   name: liquorice
-  version: 0.5.5
+  version: {{ version }}
 
 source:
-  url: https://github.com/epigen/LIQUORICE/archive/refs/tags/v0.5.5.tar.gz
+  url: https://github.com/epigen/LIQUORICE/archive/refs/tags/v{{ version }}.tar.gz
   sha256: 272c022cb0ba2e19e12823cc4d28f6ad7296733aeab55a6bb522904ced44fb8f
-  #path: ..
 
 build:
   number: 0
@@ -43,6 +44,8 @@ requirements:
     - dask ==2021.9.0
     - dask-core ==2021.9.0
     - tornado ==6.1
+    - aiohttp ==3.7.4.post0
+    - prometheus_client==0.11.0
 
 
 test:

dockerfile

@@ -1,3 +1,3 @@
 FROM condaforge/mambaforge:4.9.2-5 as conda
 
-RUN mamba install -c bioconda -c conda-forge liquorice==0.5.5 ray-core
+RUN mamba install -c bioconda -c conda-forge liquorice==0.5.6 ray-core

docs/source/conf.py

@@ -25,7 +25,7 @@
 author = 'Peter Peneder'
 
 # The full version, including alpha/beta/rc tags
-release = '0.5.5'
+release = '0.5.6'
 
 
 # -- General configuration ---------------------------------------------------

liquorice/utils/deeptoolsCountReadsPerBinDontCheckProperPairSAMflag.py

@@ -19,6 +19,7 @@
 # The only change is that the SAM flag "is_proper_pair" is not checked when determining whether a read should be
 # extended to its full fragment length. Alignment tools such as bwa mem cannot cope well with the multimodal distribution
 # of cfDNA and therefore often wrongfully call fragments not "properly_paired" if they have a size of, e.g. 350 bp.
+# In version 0.5.6 onwards an additional check results in fragments called as not properly paired if they have a template length of 0 (column 9 in bam file).
 
 def countReadsInRegions_wrapper(args):
     """
@@ -778,6 +779,8 @@ def is_proper_pair(read, maxPairedFragmentLength):
             return False
         if abs(read.template_length) > maxPairedFragmentLength:
             return False
+        if abs(read.template_length)==0: # Added for LIQUORICE v0.5.6
+            return False                 # Added for LIQUORICE v0.5.6
         # check that the mates face each other (inward)
         if read.is_reverse is read.mate_is_reverse:
             return False

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = liquorice
-version = 0.5.5
+version = 0.5.6
 author = Peter Peneder
 author_email = peter.peneder@ccri.at
 description = LIQUORICE: A tool for bias correction and quantification of changes in coverage around regions of interest in cfDNA WGS datasets