Your message dated Mon, 09 Nov 2020 23:00:10 +0000 with message-id <E1kcG8w-0002mQ-Tm@fasolo.debian.org> and subject line Bug#970447: fixed in pinfish 0.1.0+ds-1 has caused the Debian Bug report #970447, regarding ITP: pinfish -- Collection of tools to annotate genomes using long read transcriptomics data to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 970447: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=970447 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
--- Begin Message ---
- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: pinfish -- Collection of tools to annotate genomes using long read transcriptomics data
- From: Nilesh Patra <npatra974@gmail.com>
- Date: Wed, 16 Sep 2020 19:25:33 +0530
- Message-id: <CAJN1929+rpRcHb7ZQDsNKOeK4iOnADFzWW3eR6pm_T7b_=3w4w@mail.gmail.com>
Package: wnpp
Severity: wishlist
Owner: Nilesh Patra <npatra974@gmail.com>X-Debbugs-CC: debian-devel@lists.debian.org* Package name : pinfish
Version : 0.1.0+ds-1
Upstream Author : Oxford Nanopore Technologies Ltd.
* URL : https://github.com/nanoporetech/pinfish
* License : MPL-2.0
Programming Lang: GoDescription : Collection of tools to annotate genomes using long read transcriptomics data
The toolchain is composed of the following tools:
1. spliced_bam2gff - a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain.
.
2. cluster_gff - this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster.
.
3. polish_clusters - this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP.
.
4. collapse_partials - this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5' end. The tool clusters
the input transcripts into "loci" by the 3' ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.I shall maintain this package.
--- End Message ---
--- Begin Message ---
- To: 970447-close@bugs.debian.org
- Subject: Bug#970447: fixed in pinfish 0.1.0+ds-1
- From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
- Date: Mon, 09 Nov 2020 23:00:10 +0000
- Message-id: <E1kcG8w-0002mQ-Tm@fasolo.debian.org>
- Reply-to: Nilesh Patra <npatra974@gmail.com>
Source: pinfish Source-Version: 0.1.0+ds-1 Done: Nilesh Patra <npatra974@gmail.com> We believe that the bug you reported is fixed in the latest version of pinfish, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 970447@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <npatra974@gmail.com> (supplier of updated pinfish package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 16 Sep 2020 12:36:21 +0530 Source: pinfish Binary: pinfish pinfish-examples Architecture: source all amd64 Version: 0.1.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Nilesh Patra <npatra974@gmail.com> Description: pinfish - Collection of tools to annotate genomes using long read transcrip pinfish-examples - Examples and test data for pinfish Closes: 970447 Changes: pinfish (0.1.0+ds-1) unstable; urgency=medium . * Initial release (Closes: #970447) Checksums-Sha1: 3657c1e5a9587f23d8f594aeb9360a361ed35d95 2531 pinfish_0.1.0+ds-1.dsc 72cd9579ffc7d2edd6ad5429c3e934fbe3302746 68559048 pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz f60646b7255e280e7c3c5487f29707c8de208970 5054956 pinfish_0.1.0+ds.orig.tar.xz 687e69146d0534f3c83b2f5d89f11250e01080f2 6396 pinfish_0.1.0+ds-1.debian.tar.xz 415d5f7bb363a8c762db8fdccc3beaa8a66cdfeb 179336356 pinfish-examples_0.1.0+ds-1_all.deb dc6f5a19274c35d3613ac655345665208034677e 7119 pinfish_0.1.0+ds-1_amd64.buildinfo e2e31bfd8158df07044f45f85947155e8b96f7d6 1361608 pinfish_0.1.0+ds-1_amd64.deb Checksums-Sha256: 258a980b1c317679d2e090c1f63b4adbafd2b49856e3b537f58c6e21bab2f873 2531 pinfish_0.1.0+ds-1.dsc 40957e398ab9bebdc89fe69dbef1c816da544e69a6aeed9c04371430f61f53bb 68559048 pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz c8213acc3f88d9e1294b9f9014a28b8fd410ebe0aab4793c7bb7263e7e465e4d 5054956 pinfish_0.1.0+ds.orig.tar.xz d2458b758858d08d131ed657f13ae696359e1c235b439f10d54c9ae4e3bed0bb 6396 pinfish_0.1.0+ds-1.debian.tar.xz e44d12bbcee8bcd18a1aa654a18faa00bcc8f26add50ab512d0108fb26d37e26 179336356 pinfish-examples_0.1.0+ds-1_all.deb ada9c03126154f5f90d710292ea91b076c3378c50333fbd30bceef38be182de9 7119 pinfish_0.1.0+ds-1_amd64.buildinfo 9df11803e271b4d089e708c9bd29afc6506e351a0f20249951b118a2b5929eef 1361608 pinfish_0.1.0+ds-1_amd64.deb Files: 38f4d1659b3eb41772809b7cff613726 2531 science optional pinfish_0.1.0+ds-1.dsc f76133bed3fba383e81cc39b73cccdb1 68559048 science optional pinfish_0.1.0+ds.orig-debian-tests-data.tar.xz 70d87d84ead55e6112f068425ba60c56 5054956 science optional pinfish_0.1.0+ds.orig.tar.xz 720f69279d3522d3a5ebf16ae2273f40 6396 science optional pinfish_0.1.0+ds-1.debian.tar.xz 5516911da77d4065bb4618d6431a1ff8 179336356 science optional pinfish-examples_0.1.0+ds-1_all.deb e31bb21ab616d82336155402b9da36fb 7119 science optional pinfish_0.1.0+ds-1_amd64.buildinfo de5d47d6708d7969891af594028491a1 1361608 science optional pinfish_0.1.0+ds-1_amd64.deb -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+pRnYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFT7A/8CSzN5OufuowSlu8zupQsFV0apB0HcE4B uqc0R8XBC0qo7WkYrth9KvxUuIjsDc7nAbg1s4Fjx9LCDhvOxZ+VKqdw295DhATs NpeIlh44oq6xfbr8fcZXTMqvhvDm1XB5SBDGoIZfdhd1qIBe7WUTfnqTLF4wLo1A BKVHAvU2xyt0qyHqzTY+ABsspcb91yjp2amd2bEsyfCkxR4k461yEyFiqsv4p3dK R7vtsLLubVO/VpIBUOU68z45j7tLJ7wy4kYvnTYmUV8eh2Lp3WVrPh2Hpiblmio4 PomsS1MYtKDLo1E6FFlBQGAfqrJ0b/jiXdn26HG7KTYYp7ycTjVmUPMSuvFDsynK tYUtLpOWa9RSjpVCTHvLV/Ayko7+muw2IAcByrfEVynIvYl2EIuy/Z7nOnRrouC3 fVJ3FIjBYmSGtkAKVO0XiUwjACMd1qJcai/zXFpxISytlFaLRCjTNcOmVJ3TL1X0 YxKc6Br0w+XoPLFCNYGvwUX7vAigDQhME/C9qOplVIrK5OgwcHQDAdm0A3/WfuU5 DQGry6yRM6Ii0TIE1pCdhhm72MLuGj6fd/A8snwrQ0ywwNC9RDtU0Kkg65SjFGYk hg8eh3aLoIT8gUEU8y070NWK+6iUtd288tuof57iJcraYsWaKc5v3WGqfM2boReL 1EJXEtjOY+g= =2Xo1 -----END PGP SIGNATURE-----
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