From 32e5b465692388c2592ff946b19ee059fcf0f3ad Mon Sep 17 00:00:00 2001
From: Jonas Fuchs <78491186+jonas-fuchs@users.noreply.github.com>
Date: Wed, 7 Aug 2024 09:55:14 +0200
Subject: [PATCH] Fix stats (#20)

* fixed bam stats bug

* updated version
---
 bamdash/__init__.py     | 2 +-
 bamdash/command.py      | 2 +-
 bamdash/scripts/data.py | 3 +++
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/bamdash/__init__.py b/bamdash/__init__.py
index 4f4a19a..f9abe23 100644
--- a/bamdash/__init__.py
+++ b/bamdash/__init__.py
@@ -1,3 +1,3 @@
 """interactively visualize coverage and tracks"""
 _program = "bamdash"
-__version__ = "0.3"
+__version__ = "0.3.1"
diff --git a/bamdash/command.py b/bamdash/command.py
index ad7d244..de007e4 100644
--- a/bamdash/command.py
+++ b/bamdash/command.py
@@ -300,7 +300,7 @@ def main(sysargs=sys.argv[1:]):
     # dump track data
     vcf_track_count, bed_track_count, gb_track_count = 0, 0, 0
     if args.dump:
-        pd.DataFrame.from_dict(stat_dict, orient="index").to_csv("bam_stats.tabular", sep="\t", header=False, index=True)
+        pd.DataFrame.from_dict(stat_dict, orient="index").to_csv(f"{args.reference}_bam_stats.tabular", sep="\t", header=False, index=True)
         if track_data:
             for track in track_data:
                 if track[1] == "vcf":
diff --git a/bamdash/scripts/data.py b/bamdash/scripts/data.py
index 28163d4..47cef3d 100644
--- a/bamdash/scripts/data.py
+++ b/bamdash/scripts/data.py
@@ -51,6 +51,9 @@ def make_title_string(parsed_bam, coverage_df, reference, min_cov):
     stat_dict = {}
     # get bam stats for correct chrom
     bam_stats = parsed_bam.get_index_statistics()[0]
+    for bam_stats in parsed_bam.get_index_statistics():
+        if bam_stats[0] == reference:
+            break
     # pop dict
     stat_dict["reference"] = bam_stats[0]
     stat_dict["reference length (bp)"] = parsed_bam.get_reference_length(reference)