[med-svn] [Git][med-team/bustools][master] 7 commits: New upstream version 0.43.2+dfsg
Alexandre Mestiashvili (@mestia)
gitlab at salsa.debian.org
Sun Jan 14 18:03:00 GMT 2024
Alexandre Mestiashvili pushed to branch master at Debian Med / bustools
Commits:
3359162d by Alexandre Mestiashvili at 2024-01-14T10:08:48+01:00
New upstream version 0.43.2+dfsg
- - - - -
28f5ce75 by Alexandre Mestiashvili at 2024-01-14T10:08:49+01:00
Update upstream source from tag 'upstream/0.43.2+dfsg'
Update to upstream version '0.43.2+dfsg'
with Debian dir 05be7e84cc40177443cfabe79f8bdee58bf1826a
- - - - -
4cbd3b50 by Alexandre Mestiashvili at 2024-01-14T10:09:20+01:00
Update changelog
Gbp-Dch: Ignore
- - - - -
5b0942f3 by Alexandre Mestiashvili at 2024-01-14T18:43:30+01:00
d/copyright, update license from MIT to Expat for src/kseq.h
- - - - -
d06e3b50 by Alexandre Mestiashvili at 2024-01-14T18:44:51+01:00
d/patches/use-packaged-libs.patch, fix too long Description
- - - - -
68c3bb82 by Alexandre Mestiashvili at 2024-01-14T18:51:49+01:00
d/patches/inject_hardening_flags_cmake.patch, no need to forward upstream
- - - - -
48cf3d01 by Alexandre Mestiashvili at 2024-01-14T18:57:24+01:00
Update changelog, prepare for release
Gbp-Dch: Ignore
- - - - -
7 changed files:
- debian/changelog
- debian/copyright
- debian/patches/inject_hardening_flags_cmake.patch
- debian/patches/use-packaged-libs.patch
- src/Common.hpp
- src/bustools_count.cpp
- src/bustools_main.cpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+bustools (0.43.2+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 0.43.2+dfsg
+ * d/copyright, update license from MIT to Expat for src/kseq.h
+ * d/patches/use-packaged-libs.patch, fit description into 79 chars
+ * d/patches/inject_hardening_flags_cmake.patch, no need to forward upstream
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Sun, 14 Jan 2024 18:52:45 +0100
+
bustools (0.43.1+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -12,7 +12,7 @@ License: BSD-2-Clause
Files: src/kseq.h
Copyright: 2008, 2009, 2011, Attractive Chaos <attractor at live.co.uk>
-License: MIT
+License: Expat
Files: debian/*
Copyright: 2019 Alex Mestiashvili <mestia at debian.org>
@@ -41,7 +41,7 @@ License: BSD-2-Clause
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-License: MIT
+License: Expat
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
=====================================
debian/patches/inject_hardening_flags_cmake.patch
=====================================
@@ -1,6 +1,7 @@
From: Alex Mestiashvili <amestia at rsh2.donotuse.de>
Description: Patch CMakeLists.txt to inject CXXFLAGS as cmake seem to ignore
ones set with dpkg-buildflags
+Forwarded: not-needed
--- bustools.orig/CMakeLists.txt
+++ bustools/CMakeLists.txt
@@ -2,8 +2,8 @@
=====================================
debian/patches/use-packaged-libs.patch
=====================================
@@ -1,4 +1,5 @@
-Description: Use packaged libs available in our distribution instead of upstream vendored deps
+Description: Use packaged libs available in our distribution instead of
+ upstream vendored deps
Author: Nilesh Patra <nilesh at debian.org>
Forwarded: not-needed
Last-Update: 2021-07-13
=====================================
src/Common.hpp
=====================================
@@ -12,7 +12,7 @@
#include "roaring.hh"
#include "hash.hpp"
-#define BUSTOOLS_VERSION "0.43.1"
+#define BUSTOOLS_VERSION "0.43.2"
#define u_map_ std::unordered_map
enum CAPTURE_TYPE : char
=====================================
src/bustools_count.cpp
=====================================
@@ -26,7 +26,7 @@ void bustools_count(Bustools_opt &opt) {
std::vector<int32_t> tx_split; // Store transcript names for split
std::vector<int32_t> tx_split_lookup; // Map transcript IDs to mtx status
bool count_split = !opt.count_split.empty();
- int count_mtx_priority = !opt.count_gene_multimapping && count_split ? 1 : 0; // 1 = when something in tx_split overlaps something not in tx_split, prioritize the latter (useful for dealing in cases when introns of one gene overlap exons of another gene [we prioritize the exons]
+ int count_mtx_priority = (!opt.count_gene_multimapping || opt.count_collapse) && count_split ? 1 : 0; // 1 = when something in tx_split overlaps something not in tx_split, prioritize the latter (useful for dealing in cases when introns of one gene overlap exons of another gene [we prioritize the exons]
parseTranscripts(opt.count_txp, txnames);
std::vector<int32_t> genemap(txnames.size(), -1);
u_map_<std::string, int32_t> genenames;
@@ -89,9 +89,7 @@ void bustools_count(Bustools_opt &opt) {
// Essentially, we are removing all tx's that belong to (or not belong to) tx_split in the equivalence classes
// This handles instances in which a read maps to exon of one gene but intron of another (likely overlapping) gene to avoid discarding the record
// This is done at read-level (not UMI-level) so if one UMI maps to one gene's exon but another UMI maps to the other gene's intron, we still discard it
- if (count_mtx_priority == 1 && !found)
- new_ec.erase(std::remove(new_ec.begin(), new_ec.end(), tx), new_ec.end());
- else if (count_mtx_priority == 2 && found)
+ if (count_mtx_priority == 1 && found)
new_ec.erase(std::remove(new_ec.begin(), new_ec.end(), tx), new_ec.end());
}
}
=====================================
src/bustools_main.cpp
=====================================
@@ -2661,17 +2661,18 @@ void Bustools_Usage()
<< "count Generate count matrices from a BUS file" << std::endl
<< "inspect Produce a report summarizing a BUS file" << std::endl
<< "allowlist Generate an on-list from a BUS file" << std::endl
- << "project Project a BUS file to gene sets" << std::endl
+ //<< "project Project a BUS file to gene sets" << std::endl
<< "capture Capture records from a BUS file" << std::endl
- << "merge Merge bus files from same experiment" << std::endl
+ //<< "merge Merge bus files from same experiment" << std::endl
<< "text Convert a binary BUS file to a tab-delimited text file" << std::endl
+ << "fromtext Convert a tab-delimited text file to a binary BUS file" << std::endl
<< "extract Extract FASTQ reads correspnding to reads in BUS file" << std::endl
- << "predict Correct the count matrix using prediction of unseen species" << std::endl
- << "collapse Turn BUS files into a BUG file" << std::endl
- << "clusterhist Create UMI histograms per cluster" << std::endl
- << "linker Remove section of barcodes in BUS files" << std::endl
+ //<< "predict Correct the count matrix using prediction of unseen species" << std::endl
+ //<< "collapse Turn BUS files into a BUG file" << std::endl
+ //<< "clusterhist Create UMI histograms per cluster" << std::endl
+ //<< "linker Remove section of barcodes in BUS files" << std::endl
<< "compress Compress a BUS file" << std::endl
- << "inflate Decompress a BUSZ (compressed BUS) file" << std::endl
+ << "decompress Decompress a BUSZ (compressed BUS) file" << std::endl
<< "version Prints version number" << std::endl
<< "cite Prints citation information" << std::endl
<< std::endl
@@ -2787,13 +2788,13 @@ void Bustools_count_Usage()
<< "-t, --txnames File with names of transcripts" << std::endl
<< " --genecounts Aggregate counts to genes only" << std::endl
<< " --umi-gene Perform gene-level collapsing of UMIs" << std::endl
- << " --em Estimate gene abundances using EM algorithm" << std::endl
+ //<< " --em Estimate gene abundances using EM algorithm" << std::endl
<< " --cm Count multiplicities instead of UMIs" << std::endl
<< "-s, --split Split output matrix in two (plus ambiguous) based on transcripts supplied in this file" << std::endl
<< "-m, --multimapping Include bus records that pseudoalign to multiple genes" << std::endl
- << " --hist Output copy per UMI histograms for all genes" << std::endl
- << "-d --downsample Specify a factor between 0 and 1 specifying how much to downsample" << std::endl
- << " --rawcounts The count matrix will contain raw counts instead of UMI counts" << std::endl
+ //<< " --hist Output copy per UMI histograms for all genes" << std::endl
+ //<< "-d --downsample Specify a factor between 0 and 1 specifying how much to downsample" << std::endl
+ //<< " --rawcounts The count matrix will contain raw counts instead of UMI counts" << std::endl
<< std::endl;
}
@@ -3164,7 +3165,7 @@ int main(int argc, char **argv)
exit(1);
}
}
- else if (cmd == "whitelist" || cmd == "allowlist")
+ else if (cmd == "whitelist" || cmd == "allowlist" || cmd == "onlist")
{
if (disp_help)
{
View it on GitLab: https://salsa.debian.org/med-team/bustools/-/compare/bab7aeb92fb1411fed15890d7db2efd1863fddb8...48cf3d01082f1edf39ecd47ccfee5f493f191380
--
View it on GitLab: https://salsa.debian.org/med-team/bustools/-/compare/bab7aeb92fb1411fed15890d7db2efd1863fddb8...48cf3d01082f1edf39ecd47ccfee5f493f191380
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240114/0afd3840/attachment-0001.htm>
More information about the debian-med-commit
mailing list