issues
search
samtools
/
hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
http://samtools.github.io/hts-specs/
644
stars
174
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
test/vcf: Duplicate contig header record ID
#744
zaeleus
closed
5 months ago
0
Add CIGAR =/X entry to version history appendix
#743
jmarshall
closed
10 months ago
3
test/sam: Duplicate aux field tags
#742
zaeleus
closed
7 months ago
0
Modified base single letter codes update
#741
marcus1487
closed
7 months ago
7
CRAM 3.1 test data
#740
jkbonfield
closed
6 months ago
0
primary, secondary, and supplementary alignments with optional MM tags
#739
RichardCorbett
closed
1 year ago
5
VCF: "Genotype fields" vs "FORMAT" and per-sample
#738
jkbonfield
closed
5 months ago
1
What does `.` mean for an `A`, `R`, or `G` indexed field?
#737
danking
opened
1 year ago
6
Adding AEAD support as new encryption method
#736
silverdaz
opened
1 year ago
5
Consider 64-bit values in BCF, BAM and CRAM
#735
jkbonfield
opened
1 year ago
2
register bgzip in IANA media types?
#734
vidboda
closed
1 year ago
5
Circular chromosomes in the VCF header
#733
nh13
opened
1 year ago
1
sam-tags: `MM` field value pattern does not allow ambiguity codes
#732
zaeleus
opened
1 year ago
3
Revert defn of CRAM container size to be sum of block sizes (PR#731)
#731
jkbonfield
closed
1 month ago
4
VCF test case filenames should be more meaningful
#730
d-cameron
opened
1 year ago
1
Resolve #707: remove remaining *ADJ references
#729
d-cameron
closed
1 year ago
2
Can ML Tags be zero length arrays?
#728
gileshall
closed
1 year ago
5
sam: Consider recommending using 0 for mapping quality when record is unmapped
#727
zaeleus
opened
1 year ago
3
Allow for UTF-8 field values in header regular expression
#726
jmarshall
opened
1 year ago
7
sam: Consider more conventional format versioning
#725
zaeleus
opened
1 year ago
6
Document the ambiguity of 1-base long seq with QUAL *
#724
jkbonfield
opened
1 year ago
1
Fix spurious errors in test/sam/failed/aux.fail-f1.sam et al
#723
jmarshall
closed
1 year ago
1
sam: Irrelevant test failure in `aux.fail-f1.sam`
#722
zaeleus
closed
1 year ago
1
Clarify that `@RG PI` values are integers
#721
jmarshall
closed
1 year ago
4
sam: Define format of read group predicted median insert size
#720
zaeleus
closed
1 year ago
2
sam: Clarify the usage of UTF-8 characters in header
#719
zaeleus
opened
1 year ago
3
sam: Add PL value "MGIG400" as seen in the wild
#718
brainstorm
closed
1 year ago
5
vcf: Failed example has irrelevant error
#717
zaeleus
closed
4 months ago
1
vcf: Failed filter names should disallow "PASS" and MISSING
#716
zaeleus
opened
1 year ago
1
sam: Quality score ambiguity when sequence is a single base
#715
zaeleus
opened
1 year ago
2
Add an MN:i tag (number of SEQ bases at time of modification tag update).
#714
jkbonfield
closed
3 weeks ago
11
bam: Explain the use-case of the reference information section
#713
zaeleus
opened
1 year ago
2
vcf: Constrain CHROM record field with the same contig header record ID rules
#712
zaeleus
opened
1 year ago
1
vcf: Contig name rules contradiction
#711
zaeleus
opened
1 year ago
1
Storing definitions for custom tags used in SAM file
#710
cmdcolin
opened
1 year ago
1
Clarify padding base for symbolic alleles
#709
vcfer
closed
5 months ago
4
Issue with 16 bit `N CIGAR OP` field with Long Reads
#708
jonn-smith
closed
1 year ago
3
vcf: Clarify statuses of DPADJ, CNADJ, and CICNADJ INFO keys
#707
zaeleus
closed
1 year ago
0
Best encoding for use case
#706
rmhubley
closed
1 year ago
6
vcf: Define Number value P
#705
zaeleus
closed
2 months ago
7
Add a small introduction to CRAM pseudocode
#704
jkbonfield
closed
1 year ago
2
Rewrite the CRAM Base Substitution (BS) code explanation
#703
jkbonfield
closed
1 year ago
6
Spell out slice md5sums interaction with embedded references
#702
jkbonfield
closed
1 year ago
2
vcf: Valid contig ID in failed example
#701
zaeleus
opened
1 year ago
1
Fix typos (refget)
#700
jkbonfield
opened
1 year ago
0
Fix typos (VCF)
#699
jkbonfield
closed
7 months ago
1
Fix typos (Crypt4GH)
#698
jkbonfield
closed
1 year ago
0
Missing VCF 4.4 test/validation files
#697
d-cameron
opened
1 year ago
0
VCF: The "PASS" filter should be explicitly listed as optional.
#696
jkbonfield
opened
1 year ago
1
[DRAFT] Mark /github/workspace as a safe directory
#695
jkbonfield
closed
1 year ago
6
Previous
Next