[med-svn] [Git][med-team/delly][master] 4 commits: New upstream version 1.1.6

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch master at Debian Med / delly


Commits:
f1600274 by Mohammed Bilal at 2022-11-12T15:52:59+00:00
New upstream version 1.1.6
- - - - -
3498b1e1 by Mohammed Bilal at 2022-11-12T15:52:59+00:00
routine-update: New upstream version

- - - - -
ba92d35a by Mohammed Bilal at 2022-11-12T15:53:02+00:00
Update upstream source from tag 'upstream/1.1.6'

Update to upstream version '1.1.6'
with Debian dir 437bdeb33f7a9a6c94ba80d83ad2f5700d5b8ccd
- - - - -
a1a2e66e by Mohammed Bilal at 2022-11-12T15:55:00+00:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- Dockerfile
- Makefile
- debian/changelog
- parallel/Dockerfile
- singularity/delly.def
- src/filter.h
- src/version.h


Changes:

=====================================
Dockerfile
=====================================
@@ -1,5 +1,5 @@
 # use the ubuntu base image
-FROM ubuntu:18.04
+FROM ubuntu:22.04
 
 MAINTAINER Tobias Rausch rausch at embl.de
 
@@ -19,6 +19,7 @@ RUN apt-get update && apt-get install -y \
     libboost-filesystem-dev \
     libboost-iostreams-dev \
     libbz2-dev \
+    libdeflate-dev \
     libhdf5-dev \
     libncurses-dev \
     liblzma-dev \


=====================================
Makefile
=====================================
@@ -25,7 +25,7 @@ endif
 
 # Flags for static compile
 ifeq (${STATIC}, 1)
-	LDFLAGS += -static -static-libgcc -pthread -lhts -lz -llzma -lbz2
+	LDFLAGS += -static -static-libgcc -pthread -lhts -lz -llzma -lbz2 -ldeflate
 else
 	LDFLAGS += -lhts -lz -llzma -lbz2 -Wl,-rpath,${EBROOTHTSLIB}
 endif


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+delly (1.1.6-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Mohammed Bilal <mdbilal at disroot.org>  Sat, 12 Nov 2022 15:53:21 +0000
+
 delly (1.1.5-1) unstable; urgency=medium
 
   * Team upload.


=====================================
parallel/Dockerfile
=====================================
@@ -1,5 +1,5 @@
 # use the ubuntu base image
-FROM ubuntu:18.04
+FROM ubuntu:22.04
 
 MAINTAINER Tobias Rausch rausch at embl.de
 
@@ -19,6 +19,7 @@ RUN apt-get update && apt-get install -y \
     libboost-filesystem-dev \
     libboost-iostreams-dev \
     libbz2-dev \
+    libdeflate-dev \
     libhdf5-dev \
     libncurses-dev \
     liblzma-dev \


=====================================
singularity/delly.def
=====================================
@@ -1,11 +1,11 @@
 # Build image
 BootStrap: library
-From: ubuntu:16.04
+From: ubuntu:22.04
 Stage: build
 
 %post
 	apt-get -y update
-	apt-get install -y autoconf build-essential cmake g++ gfortran git libcurl4-gnutls-dev hdf5-tools libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev libbz2-dev libhdf5-dev libncurses-dev liblzma-dev zlib1g-dev
+	apt-get install -y autoconf build-essential cmake g++ gfortran git libcurl4-gnutls-dev hdf5-tools libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev libbz2-dev libhdf5-dev libncurses-dev liblzma-dev zlib1g-dev libdeflate-dev
 	apt-get clean
 	rm -rf /var/lib/apt/lists/*
 	cd /opt


=====================================
src/filter.h
=====================================
@@ -48,6 +48,7 @@ struct FilterConfig {
   int32_t minsize;
   int32_t maxsize;
   int32_t coverage;
+  int32_t qualthres;
   float ratiogeno;
   float altaf;
   float controlcont;
@@ -134,7 +135,7 @@ filterRun(TFilterConfig const& c) {
     if (svend != NULL) svlen = *svend - rec->pos;
     int32_t inslenVal = 0;
     if (bcf_get_info_int32(hdr, rec, "INSLEN", &inslen, &ninslen) > 0) inslenVal = *inslen;
-    if ((pass) && ((std::string(svt) == "BND") || ((std::string(svt) == "INS") && (inslenVal >= c.minsize) && (inslenVal <= c.maxsize)) || ((std::string(svt) != "BND") && (std::string(svt) != "INS") && (svlen >= c.minsize) && (svlen <= c.maxsize)))) {
+    if ((rec->qual >= c.qualthres) && (pass) && ((std::string(svt) == "BND") || ((std::string(svt) == "INS") && (inslenVal >= c.minsize) && (inslenVal <= c.maxsize)) || ((std::string(svt) != "BND") && (std::string(svt) != "INS") && (svlen >= c.minsize) && (svlen <= c.maxsize)))) {
       // Check genotypes
       bcf_unpack(rec, BCF_UN_ALL);
       bool precise = false;
@@ -299,7 +300,8 @@ int filter(int argc, char **argv) {
     ("help,?", "show help message")
     ("filter,f", boost::program_options::value<std::string>(&c.filter)->default_value("somatic"), "Filter mode (somatic, germline)")
     ("outfile,o", boost::program_options::value<boost::filesystem::path>(&c.outfile), "Filtered SV BCF output file")
-    ("altaf,a", boost::program_options::value<float>(&c.altaf)->default_value(0.2), "min. fractional ALT support")
+    ("quality,y", boost::program_options::value<int32_t>(&c.qualthres)->default_value(300), "min. SV site quality")
+    ("altaf,a", boost::program_options::value<float>(&c.altaf)->default_value(0.03), "min. fractional ALT support")
     ("minsize,m", boost::program_options::value<int32_t>(&c.minsize)->default_value(0), "min. SV size")
     ("maxsize,n", boost::program_options::value<int32_t>(&c.maxsize)->default_value(500000000), "max. SV size")
     ("ratiogeno,r", boost::program_options::value<float>(&c.ratiogeno)->default_value(0.75), "min. fraction of genotyped samples")


=====================================
src/version.h
=====================================
@@ -5,7 +5,7 @@ namespace torali
 {
 
 
-  std::string dellyVersionNumber = "1.1.5";
+  std::string dellyVersionNumber = "1.1.6";
 
   inline 
     void printTitle(std::string const& title) 



View it on GitLab: https://salsa.debian.org/med-team/delly/-/compare/3a0544cf2d2ccd0b4a22a461a2cd55ac185be7a5...a1a2e66e640a492f25cf9ed839cd966eb3162dc4

-- 
View it on GitLab: https://salsa.debian.org/med-team/delly/-/compare/3a0544cf2d2ccd0b4a22a461a2cd55ac185be7a5...a1a2e66e640a492f25cf9ed839cd966eb3162dc4
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