From 8fe0cbe78965f54f7c293fccded1801f6367b322 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <mate.balajti@unibas.ch>
Date: Thu, 18 Jan 2024 11:10:07 +0100
Subject: [PATCH] update comments in mapping

---
 htsinfer/mapping.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/htsinfer/mapping.py b/htsinfer/mapping.py
index e1cef46..52780f3 100644
--- a/htsinfer/mapping.py
+++ b/htsinfer/mapping.py
@@ -51,11 +51,7 @@ def __init__(
         self.star_dirs: List[Path] = []
 
     def evaluate(self):
-        """Infer read orientation.
-
-        Returns:
-            Orientation results object.
-        """
+        """Align FASTQ files to reference transcripts with STAR."""
 
         # get transcripts for current organims
         transcripts = self.subset_transcripts_by_organism()
@@ -270,6 +266,10 @@ def prepare_star_alignment_commands(
     ) -> Dict[Path, List[str]]:
         """Prepare STAR alignment commands.
 
+        Input FASTQ files are assumed to be sorted according to reference names
+        or coordinates, the order of input reads is kept with the option
+        "PairedKeepInputOrder", no additional sorting of aligned reads is done.
+
         Args:
             index_dir: Path to directory containing STAR index.