Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

changeset 12:02874b1b2015 draft

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Uploaded
author jackcurragh
date Wed, 02 Nov 2022 15:23:28 +0000
parents 3d2b1532a1b0
children df4bb52b226d
files trips_bam_to_sqlite/bam_to_sqlite.py trips_bam_to_sqlite/trips_bam_to_sqlite.xml
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/trips_bam_to_sqlite/bam_to_sqlite.py	Wed Nov 02 14:52:17 2022 +0000
+++ b/trips_bam_to_sqlite/bam_to_sqlite.py	Wed Nov 02 15:23:28 2022 +0000
@@ -251,7 +251,7 @@
 	master_metagene_stop_dict = {"fiveprime":{}, "threeprime":{}}
 
 
-	os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam')
+	os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam 2> /dev/null')
 
 	pysam.set_verbosity(0)
 	infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
--- a/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Wed Nov 02 14:52:17 2022 +0000
+++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Wed Nov 02 15:23:28 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.5">
+<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.5.1">
     <description>Convert BAM file to SQLITE for Trips-Viz</description>
     <requirements>
         <requirement type="package" version="0.19.0">pysam</requirement>