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sstadick / perbase

Per-base per-nucleotide depth analysis
MIT License
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Index out of bounds #68

Open ChristopherRichie opened 9 months ago

ChristopherRichie commented 9 months ago

Hi Sstadick,

FIRST, thanks for sharing this program, I have been looking for this since I got my ONT Minion... I do not know how I have missed it over the past several years, but today my Google search unlocked something.

I have a question about the "index out of bounds" that I think is similar to issue #53.

I had four CRAM files (and matching sorted BAMs) and a reference... some of them failed on the basic command: perbase base-depth [cram] or perbase base-depth [bam]

These same files did work, and produced results, when I included the -F 260 flag.

Can you clarify what is excluded when I use the -F 260 parameter? as in: perbase base-depth BC06_SAMPLE.pass.cram -r CR2839_ref.fa --output BC06.tsv -F 260

I think that it would exclude any unmapped reads and/or any reads that are not in the primary alignment. (This situation would be ok for my intended use case.)

Thanks again. this code lets me avoid showing BAM alignments through IGV at lab meeting, and lets me boil them down into line graphs... THANKS

sstadick commented 9 months ago

Hi! Sorry for the delay in reply, I'm not sure how I missed the notifications. You are correct that -F 260 will exclude any unmapped or reads that are not primary alignment. It's using the htslib engine under the hood the same as samtools, those flags act the same way.

If that works for you I'm probably not going to have time to dig into this a lot further in the near future. It's been a while since I've been in the code here!

ChristopherRichie commented 9 months ago

No problem. "as is" this analysis is giving me good results.

I do not find any "instructions" for citing your work. I appreciate that you are not actively developing this code, but if there is specific language you would prefer for acknowledgement, please let me know.

Thanks!

From: Seth @.> Sent: Monday, October 9, 2023 3:43 PM To: sstadick/perbase @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [sstadick/perbase] Index out of bounds (Issue #68)

Hi! Sorry for the delay in reply, I'm not sure how I missed the notifications. You are correct that -F 260 will exclude any unmapped or reads that are not primary alignment. It's using the htslib engine under the hood the same as samtools, those flags act the same way.

If that works for you I'm probably not going to have time to dig into this a lot further in the near future. It's been a while since I've been in the code here!

- Reply to this email directly, view it on GitHubhttps://github.com/sstadick/perbase/issues/68#issuecomment-1753615627, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQZL33RIJD5CFZDTAWDX6RHSRAVCNFSM6AAAAAA5RTW2HGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJTGYYTKNRSG4. You are receiving this because you authored the thread.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

sstadick commented 9 months ago

Hi! I appreciate the ask about citations! Nobody has asked about that before. I've added a Citation file and there should now be a Cite the repository button on the sidebar of the main page. I have no specific language to add to what it auto generates. 

Stadick, S. (2023). Perbase (Version 0.9.0) [Computer software]
ChristopherRichie commented 9 months ago

I very much appreciate the code you've shared. Thanks!

From: Seth @.> Sent: Wednesday, October 11, 2023 11:15 AM To: sstadick/perbase @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [sstadick/perbase] Index out of bounds (Issue #68)

Hi! I appreciate the ask about citations! Nobody has asked about that before. I've added a Citation file and there should now be a Cite the repository button on the sidebar of the main page. I have no specific language to add to what it auto generates.

Stadick, S. (2023). Perbase (Version 0.9.0) [Computer software]

- Reply to this email directly, view it on GitHubhttps://github.com/sstadick/perbase/issues/68#issuecomment-1757924452, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQ724ODK2IBCENRJ7ZLX62ZXVANCNFSM6AAAAAA5RTW2HE. You are receiving this because you authored the thread.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.