From b13b1931e865c6f0bddeea14423393fd3a4ffcab Mon Sep 17 00:00:00 2001
From: e-sollier <etienne.sollier@gmail.com>
Date: Thu, 30 Jan 2025 19:22:12 +0100
Subject: [PATCH] Avoid errors when some reads are missing MM/ML tags

---
 figeno/cli/cli.py            | 2 +-
 figeno/gui/package-lock.json | 4 ++--
 figeno/gui/package.json      | 2 +-
 figeno/track_basemodfreq.py  | 2 ++
 pyproject.toml               | 2 +-
 5 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/figeno/cli/cli.py b/figeno/cli/cli.py
index 362ce60..a0a5e36 100644
--- 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
index 6e0f93c..a8362e0 100644
--- a/figeno/gui/package-lock.json
+++ b/figeno/gui/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "figeno",
-  "version": "1.6.2",
+  "version": "1.6.5",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "figeno",
-      "version": "1.6.2",
+      "version": "1.6.5",
       "dependencies": {
         "@dnd-kit/core": "^6.1.0",
         "@dnd-kit/sortable": "^8.0.0",
diff --git a/figeno/gui/package.json b/figeno/gui/package.json
index 8825e46..1b15efc 100644
--- 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
index 4a78413..e8b2f19 100644
--- 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
index 6a63ffa..e382dfa 100644
--- 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 = [