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indel length not display #1945

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coopsor opened this issue Mar 4, 2025 · 1 comment
Open

indel length not display #1945

coopsor opened this issue Mar 4, 2025 · 1 comment

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@coopsor
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coopsor commented Mar 4, 2025

When viewing my BAM files in IGV-Web, the specific INDEL length information is not displayed, which is inconsistent with the IGV-desktop version. How can I make it consistent with the IGV-desktop version display? Looking for your reply!
igv-web snapshot:
Image
igv-desktop:
Image

The key difference is that IGV-Web has slightly different settings and capabilities compared to the desktop version. So how to modify the settings to match the desktop version's INDEL display?

here is my python code about igv display:

def send_command(sock, command):
    print(f"发送命令: {command}")
    sock.send(command.encode() + b'\n')

    return True

send_command(sock, f'load {bam_file}')
send_command(sock, 'preference SAM.SHOW_SMALL_INDELS true') 
send_command(sock, 'preference SAM.SMALL_INDEL_BP_THRESHOLD 50')


for chrom, start, end, name in region_list:
    start, end = start - (end-start)//2, end + (end-start)//2 
    send_command(sock, f'goto {chrom}:{start}-{end}')
    send_command(sock, 'snapshotSize 800')
    send_command(sock, 'collapse')
    snapshot_file = f'{output_dir}/{name}_{index}.png'
    send_command(sock, f'snapshot {snapshot_file}')

@jrobinso
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jrobinso commented Mar 4, 2025

That's not currently a feature of igv-web. There is no way to match the desktop in this instance, they are different software.

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