Fix reference
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 20/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics, cli
Research direction
Start by reproducing the two supplied bcftools +fixref commands with the referenced BCF, FASTA, and VCF inputs, then inspect the reported BGZF offset and input files. Done means identifying whether the failure is a tool defect or an input-file problem and documenting the supported correction.
Written by the indexing model from the issue text.
Description
Hi,
I want to fix my data with the reference data using bcftools. However, I am getting the following error "[E::bgzf_read_block] Failed to read BGZF block data at offset 33357268 expected 7939 bytes; hread returned 538" when I run the following commands
./bcftools +fixref /path/mydatabcf -Ob -o /path/mydata-RefFixed.bcf -- -d -f $REF/human_g1k_v37.fasta.gz -i $REF/All_20170710.vcf.gz
./bcftools +fixref /path/mydata-RefFixed.bcf -- -f $REF/human_g1k_v37.fasta.gz
Could you please help me with this error?
Thank you very much.
Best,
Sonali
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from samtools/bcftools
-
needs-feedback
Difficulty 3/5 1-2 days Newbie friendliness 55/100
-
enhancement
Difficulty 5/5 Over a week Newbie friendliness 45/100
-
htslib-dependent P2: Desirable
Difficulty 3/5 1-2 days Newbie friendliness 48/100
-
Difficulty 5/5 Over a week Newbie friendliness 30/100
-
needs-feedback requires-test-case
Difficulty 3/5 1-2 days Newbie friendliness 55/100
All issues in samtools/bcftools
Similar issues
-
[adam] AdamNet network read doesn't cap to MAX_ADAM_PACKET_LEN, overflows client receive buffers Open
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
FujiNetWIFI/fujinet-firmware#1649 · 2 comments ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
HarbourMasters/Shipwright#7229 ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 72/100
riscv-software-src/riscv-isa-sim#2435 · 1 comment ·
-
bug Self Built Image SNAPSHOT Supported Device target/ramips
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
-
Difficulty 2/5 1-3 hours Newbie friendliness 76/100