Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
diff trips_bam_to_sqlite/bam_to_sqlite.py @ 6:1be4bbe849e3 draft
Uploaded
author | jackcurragh |
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date | Tue, 07 Jun 2022 16:20:36 +0000 |
parents | 4ee95ba271a5 |
children | 2c6f630c732f |
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--- a/trips_bam_to_sqlite/bam_to_sqlite.py Fri May 27 10:14:00 2022 +0000 +++ b/trips_bam_to_sqlite/bam_to_sqlite.py Tue Jun 07 16:20:36 2022 +0000 @@ -288,9 +288,8 @@ master_offset_dict = {"fiveprime": {}, "threeprime": {}} master_metagene_stop_dict = {"fiveprime": {}, "threeprime": {}} - os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam') pysam.set_verbosity(0) - infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb") + infile = pysam.Samfile(f"{bam_filepath}", "rb") header = infile.header["HD"] unsorted = False if "SO" in header: