From aa5c9ba9d1081be9aa8f92fe3fd03c7dc1be8fb7 Mon Sep 17 00:00:00 2001
From: Chang Ye <yech1990@gmail.com>
Date: Tue, 2 Jul 2024 00:06:32 -0500
Subject: [PATCH] release 0.0.49

---
 cutseq/run.py  | 27 +++++++++++++++++++++++----
 pyproject.toml |  2 +-
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/cutseq/run.py b/cutseq/run.py
index 8d30826..dca6ff7 100644
--- a/cutseq/run.py
+++ b/cutseq/run.py
@@ -23,6 +23,7 @@
     SuffixAdapter,
 )
 from cutadapt.files import InputPaths, OutputFiles
+from cutadapt.info import ModificationInfo
 from cutadapt.modifiers import (
     AdapterCutter,
     PairedEndRenamer,
@@ -79,6 +80,24 @@ def test(self, read, info):
         return False
 
 
+class ConditionalCutter(SingleEndModifier):
+    def __init__(self, length: int):
+        self.length = length
+
+    def __repr__(self):
+        return f"ConditionalCutter(length={self.length})"
+
+    def __call__(self, read, info: ModificationInfo):
+        if not info.matches:
+            return read
+        if self.length > 0:
+            info.cut_prefix = read.sequence[: self.length]
+            return read[self.length :]
+        elif self.length < 0:
+            info.cut_suffix = read.sequence[self.length :]
+            return read[: self.length]
+
+
 class ReverseComplementConverter(SingleEndModifier):
     def __init__(self):
         self.rcd = False
@@ -548,7 +567,7 @@ def pipeline_paired(
                 UnconditionalCutter(barcode.umi5.len),
                 UnconditionalCutter(-barcode.umi5.len)
                 if settings.read_through
-                else None,
+                else ConditionalCutter(-barcode.umi5.len),
             ),
         )
     if barcode.umi3.len > 0:
@@ -556,7 +575,7 @@ def pipeline_paired(
             (
                 UnconditionalCutter(-barcode.umi3.len)
                 if settings.read_through
-                else None,
+                else ConditionalCutter(-barcode.umi3.len),
                 UnconditionalCutter(barcode.umi3.len),
             )
         )
@@ -572,7 +591,7 @@ def pipeline_paired(
                 UnconditionalCutter(barcode.mask5.len),
                 UnconditionalCutter(-barcode.mask5.len)
                 if settings.read_through
-                else None,
+                else ConditionalCutter(-barcode.mask5.len),
             )
         )
     if barcode.mask3.len > 0:
@@ -580,7 +599,7 @@ def pipeline_paired(
             (
                 UnconditionalCutter(-barcode.mask3.len)
                 if settings.read_through
-                else None,
+                else ConditionalCutter(-barcode.mask3.len),
                 UnconditionalCutter(barcode.mask3.len),
             )
         )
diff --git a/pyproject.toml b/pyproject.toml
index e520a0b..0e930b0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cutseq"
-version = "0.0.48"
+version = "0.0.49"
 description = "Automatically cut adapter / barcode / UMI from NGS data"
 authors = ["Ye Chang <yech1990@gmail.com>"]
 license = "MIT"