Avoid errors when some reads are missing MM/ML tags

CompEpigen · Jan 30, 2025 · b13b193 · b13b193
1 parent 9f3eb48
commit b13b193
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Showing 5 changed files with 7 additions and 5 deletions.
diff --git a/figeno/cli/cli.py b/figeno/cli/cli.py
@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.6.5"
+__version__ = "1.6.6"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

diff --git a/figeno/gui/package-lock.json b/figeno/gui/package-lock.json
diff --git a/figeno/gui/package.json b/figeno/gui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.6.5",
+  "version": "1.6.6",
   "private": true,
   "homepage": "./",
   "dependencies": {

diff --git a/figeno/track_basemodfreq.py b/figeno/track_basemodfreq.py
@@ -236,6 +236,8 @@ def create_basemod_table_bam(reads,base,mod,chr,start,end,samfile=None,fix_hardc
     pos2unmethylated={}
     for x in reads:
         for read in x:
+            if (not read.has_tag("MM")) or (not read.has_tag("ML")):
+                continue
             methyl = decode_read_basemods(read,[(base,mod,1)],samfile,fix_hardclip,warnings=warnings)
             for pos,end2,state in methyl:
                 if base=="C" and (read.flag&16)!=0:

diff --git a/pyproject.toml b/pyproject.toml
@@ -9,7 +9,7 @@ packages = ["figeno", "figeno.data", "figeno.cli", "figeno.gui"]
 
 [project]
 name = 'figeno'
-version = "1.6.5"
+version = "1.6.6"
 description = 'Package for generating genomics figures.'
 readme = 'README.md'
 authors = [