Releases: compgen-io/ngsutilsj
Minor updates
Added a few new commands and added support for bgzip compressed FASTA files (indexed with samtools faidx)
What's Changed
- Added option for doing FASTA motif searches by sequence instead of PWM. by @mbreese in #17
- Cleanup of fasta-motif code by @mbreese in #18
Full Changelog: ngsutilsj-0.5.3...ngsutilsj-0.5.5
Contributors
Assets 4
Current production release v0.5.0
This version adds significant updates for working with neoantigens / peptides. vcf-peptide will use a VCF file to find all potential neo-peptides in a protein. vcf-effect will annotate variants with their effect (somewhat limited), gtf-tofasta can be used to export gene / transcript / protein sequences for genes based on GTF gene model
Current production release
Contributors
Assets 4
Current production release
ngsutilsj-0.4.10 Current production version
ngsutilsj-0.4.8
Many updates for VCF and tab-delimited annotations.
Added ability to check a FASTQ file for completeness and MD5/SHA1 hash at the same time.
Also added bam-removeclipping as an option for BAM files.
Full notes:
commit 0c4f7c5 (HEAD -> master, tag: ngsutilsj-0.4.8, origin/master)
Date: Thu Aug 22 12:25:48 2019 -0400
version bump
commit 1fa8c0a
Date: Thu Aug 22 12:23:11 2019 -0400
Added hidden BAI reader (for future use)
commit 4e636ae
Date: Thu Aug 22 12:20:48 2019 -0400
Ported remove-clipping function back
commit 3272134
Date: Fri Aug 16 11:57:41 2019 -0400
Added a cache for reading individual blocks / offsets.
This doesn't actually cache specific BGZ blocks, but rather the results
from the full pos/offset query. This lets us cache specific intervals
of the BGZ chunks, without worrying about trying to manage filepointers
with the cache.
commit 08311a8
Date: Thu Aug 8 23:26:45 2019 -0400
added an option to skip chromosomes missing in BAM file but that were
present in the VCF file.
Can now use a male VCF file (XY) to count a female BAM file (XX)
commit 33e943f
Date: Thu Aug 8 19:11:58 2019 -0400
Updated vcf-chrfix to allow more changes based on contig/chrom.
Refactored ##contig== lines to their own handler.
commit d2001a6
Date: Wed Aug 7 11:22:30 2019 -0400
doc update
commit 02349ae
Date: Fri Aug 2 11:16:09 2019 -0400
Progress messages can't parse skipped lines in a tabix file.
commit f74f8ad
Date: Fri Aug 2 11:15:15 2019 -0400
Added a verbose message about the index, if available.
commit 7b89934
Date: Wed Jul 31 14:42:15 2019 -0400
typo in trimming a single sequence.
commit cc1fd8b
Date: Tue Jul 23 18:58:39 2019 -0400
Added doc to illumina trim
commit c2b248b
Merge: 9518e84 2190988
Date: Thu Jul 11 22:09:45 2019 -0400
Merge branch 'master' of git@github.com:compgen-io/ngsutilsj.git
Conflicts:
src/java/io/compgen/ngsutils/cli/bam/BamBest.java
commit 9518e84
Date: Thu Jul 11 21:52:47 2019 -0400
Added --unmapped option for bam-best
commit 2190988
Date: Thu Jul 11 21:52:47 2019 -0400
Added --unmapped option for bam-best
commit 597fcd8
Date: Wed May 22 22:58:32 2019 -0400
fastq-check had NPE when not checking MD5 at the same time.
commit de4b6e3
Date: Wed May 22 22:58:09 2019 -0400
added a cache for tabix-annotations
commit d48a383
Date: Wed May 22 12:07:31 2019 -0400
Bugfix - progress bar wasn't showing end-pos...
commit 807cc28
Date: Wed May 22 12:05:55 2019 -0400
Added progress bar to tab-annotate
commit 05aa11e
Date: Sat Apr 13 12:39:23 2019 -0400
Added MD5/SHA1/SHA256 options for verifying FASTQ
File hashes will be verified at the same time as running fastq-check to
validate the records / gzip.
ngsutilsj-0.4.7
Added rec.isIndel(), and updated vcf-export and vcf-strip to use it.