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  1. UGENE
  2. UGENE-6755

Opening a BAM or SAM file with dots in the file name

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Cannot Reproduce
    • Affects Version/s: 34
    • Fix Version/s: None
    • Component/s: NGS
    • Labels:
    • Story Points:
      2
    • Sprint:
      DEV-35-1
    • Affect Type:
      Userdefined

      Description

      When a BAM file has dots in the file name, the corresponding *.bai (the index file) is not read properly. For example, download "chrM.sorted.bam" and "chrM.sorted.bam.bai" files, put them into the same folder. When the bam file is opened, there is a message in the import BAM file dialog, see the screenshot.

        Attachments

        1. chrM.sorted.bam
          2.00 MB
          Olga Golosova
        2. chrM.sorted.bam.bai
          0.1 kB
          Olga Golosova
        3. problem-with-bam-file-index.png
          109 kB
          Olga Golosova

          Issue Links

          relates to

          Bug - A problem which impairs or prevents the functions of the product. UGENE-2760 An error occurs when converting bam to ugenedb on some systems

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. UGENE-4065 Embedded samtools can't find prebuilt index if its path contains "bam"

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-4774 Remove index verification on opening BAM files

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              ichebykin Igor Chebykin [X] (Inactive)
              Reporter:
              oigl Olga Golosova
              Watchers:
              0 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: