[med-svn] [Git][med-team/lumpy-sv][master] 9 commits: Remove copyright

Nilesh Patra gitlab at salsa.debian.org
Fri Sep 18 21:10:16 BST 2020 


Nilesh Patra pushed to branch master at Debian Med / lumpy-sv


Commits:
558eb2e3 by Nilesh Patra at 2020-09-18T18:58:51+00:00
Remove copyright

- - - - -
59fabdf7 by Nilesh Patra at 2020-09-18T18:59:17+00:00
Add sam files for repacked bam files

- - - - -
8c3bee8a by Nilesh Patra at 2020-09-18T19:02:33+00:00
New upstream version 0.3.1+dfsg
- - - - -
0d9eb0f4 by Nilesh Patra at 2020-09-18T19:02:34+00:00
Update upstream source from tag 'upstream/0.3.1+dfsg'

Update to upstream version '0.3.1+dfsg'
with Debian dir 9acfdd832b29d2d1b0761b49b4b80c1d2d898fea
- - - - -
bf277e88 by Nilesh Patra at 2020-09-19T00:49:18+05:30
Generate bam files during build

- - - - -
7b20fa30 by Nilesh Patra at 2020-09-19T01:14:17+05:30
Append -g flag

- - - - -
63ff3101 by Nilesh Patra at 2020-09-19T01:14:53+05:30
Add myself to uploaders

- - - - -
11f54e61 by Nilesh Patra at 2020-09-19T01:15:44+05:30
Update changelog

- - - - -
152e14e3 by Nilesh Patra at 2020-09-19T01:16:36+05:30
routine-update: Ready to upload to unstable

- - - - -


12 changed files:

- − data/pe.pos_sorted.bam
- − data/sr.pos_sorted.bam
- debian/changelog
- debian/control
- debian/copyright
- + debian/missing-sources/pe.pos_sorted.sam
- + debian/missing-sources/sr.pos_sorted.sam
- debian/patches/use_debian_packaged_libs.patch
- debian/rules
- src/filter/filter.c
- src/lumpy/SV_Pair.cpp
- src/lumpy/SV_Pair.h


Changes:

=====================================
data/pe.pos_sorted.bam deleted
=====================================
Binary files a/data/pe.pos_sorted.bam and /dev/null differ


=====================================
data/sr.pos_sorted.bam deleted
=====================================
Binary files a/data/sr.pos_sorted.bam and /dev/null differ


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+lumpy-sv (0.3.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 0.3.1+dfsg
+  * Add sam files for repacked bam files
+  * Generate bam files during build
+  * Append -g flag
+  * Add myself to uploaders
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sat, 19 Sep 2020 01:16:36 +0530
+
 lumpy-sv (0.3.0+dfsg-2) unstable; urgency=medium
 
   * debhelper-compat 13 (routine-update)


=====================================
debian/control
=====================================
@@ -1,6 +1,6 @@
 Source: lumpy-sv
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <npatra974 at gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
@@ -12,7 +12,8 @@ Build-Depends: debhelper-compat (= 13),
                libsqlite3-dev,
                libhts-dev,
                libssl-dev,
-               libcurl4-openssl-dev | libcurl4-dev
+               libcurl4-openssl-dev | libcurl4-dev,
+               samtools
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv
 Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git


=====================================
debian/copyright
=====================================
@@ -6,6 +6,7 @@ Files-Excluded: */BamTools
                 */gzstream
                 */sqlite3
                 */.git*
+                */*.bam
 
 Files: *
 Copyright: 2011-2014 Ryan M. Layer


=====================================
debian/missing-sources/pe.pos_sorted.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/sr.pos_sorted.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -7,7 +7,7 @@ Description: Use Debian packaged libraries
 
 --- a/Makefile
 +++ b/Makefile
-@@ -24,21 +24,18 @@ endif
+@@ -24,21 +24,18 @@
  #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC 
  export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC 
  export LIBS		= -lz -L $(ZLIB_PATH)
@@ -30,7 +30,7 @@ Description: Use Debian packaged libraries
  
  
  all:	lumpy_filter lumpyexpress lumpy
-@@ -50,9 +47,9 @@ lumpy:
+@@ -50,9 +47,9 @@
  	@echo "Building lumpy:"
  	@echo "========================================================="
  
@@ -42,7 +42,7 @@ Description: Use Debian packaged libraries
  		echo "- Building in $$dir"; \
  		$(MAKE) --no-print-directory -C $$dir; \
  		echo ""; \
-@@ -64,7 +61,7 @@ lumpy:
+@@ -64,7 +61,7 @@
  		echo ""; \
  	done
  
@@ -51,7 +51,7 @@ Description: Use Debian packaged libraries
  	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
  	$(MAKE) --no-print-directory -C src/filter/
  	cp src/filter/lumpy_filter $(BIN_DIR)
-@@ -100,9 +97,9 @@ lumpyexpress:
+@@ -100,9 +97,9 @@
  clean:
  	@echo "Cleaning up."
  	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@@ -67,7 +67,7 @@ Description: Use Debian packaged libraries
  .PHONY: clean
 --- a/src/lumpy/Makefile
 +++ b/src/lumpy/Makefile
-@@ -9,14 +9,13 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+@@ -9,14 +9,13 @@
             -I$(UTILITIES_DIR)/bedFilePE/ \
             -I$(UTILITIES_DIR)/genomeFile/ \
             -I$(UTILITIES_DIR)/version/ \
@@ -85,7 +85,7 @@ Description: Use Debian packaged libraries
  
  # ----------------------------------
  # define our source and object files
-@@ -39,12 +38,10 @@ SOURCES= lumpy.cpp \
+@@ -39,12 +38,10 @@
  OBJECTS= $(SOURCES:.cpp=.o)
  _EXT_OBJECTS=BamAncillary.o \
  			 sequenceUtils.o \
@@ -99,7 +99,7 @@ Description: Use Debian packaged libraries
  EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
  BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
  PROGRAM=lumpy
-@@ -54,24 +51,25 @@ all: $(PROGRAM)
+@@ -54,24 +51,25 @@
  
  $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
  	@echo "  * linking $(PROGRAM)"
@@ -142,11 +142,11 @@ Description: Use Debian packaged libraries
  
  all:
 -	$(CC) -I../../lib/htslib/ -o lumpy_filter filter.c ../../lib/htslib/libhts.a -lcrypto -lcurl -lpthread -lz
-+	$(CC) -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
++	$(CC) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
  
 --- a/src/utils/genomeFile/Makefile
 +++ b/src/utils/genomeFile/Makefile
-@@ -6,7 +6,7 @@ UTILITIES_DIR = ../
+@@ -6,7 +6,7 @@
  # -------------------
  INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
             -I$(UTILITIES_DIR)/fileType/ \
@@ -157,7 +157,7 @@ Description: Use Debian packaged libraries
  # define our source and object files
 --- a/src/utils/BamTools-Ancillary/Makefile
 +++ b/src/utils/BamTools-Ancillary/Makefile
-@@ -2,10 +2,9 @@ OBJ_DIR = ../../../obj/
+@@ -2,10 +2,9 @@
  BIN_DIR = ../../../bin/
  UTILITIES_DIR = ../
  
@@ -169,7 +169,7 @@ Description: Use Debian packaged libraries
             -I$(UTILITIES_DIR)/fileType/
  
  # ----------------------------------
-@@ -27,4 +26,4 @@ clean:
+@@ -27,4 +26,4 @@
  	@echo "Cleaning up."
  	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
  
@@ -178,7 +178,7 @@ Description: Use Debian packaged libraries
 +.PHONY: clean
 --- a/src/utils/BlockedIntervals/Makefile
 +++ b/src/utils/BlockedIntervals/Makefile
-@@ -2,9 +2,8 @@ OBJ_DIR = ../../../obj/
+@@ -2,9 +2,8 @@
  BIN_DIR = ../../../bin/
  UTILITIES_DIR = ../
  
@@ -189,7 +189,7 @@ Description: Use Debian packaged libraries
             -I$(UTILITIES_DIR)/fileType/ \
             -I$(UTILITIES_DIR)/lineFileUtilities/
  
-@@ -13,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/BamTools/i
+@@ -13,7 +12,7 @@
  # ----------------------------------
  SOURCES= BlockedIntervals.cpp BlockedIntervals.h
  OBJECTS= $(SOURCES:.cpp=.o)
@@ -198,7 +198,7 @@ Description: Use Debian packaged libraries
  EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
  BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
  
-@@ -32,4 +31,4 @@ clean:
+@@ -32,4 +31,4 @@
  	@echo "Cleaning up."
  	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
  
@@ -207,7 +207,7 @@ Description: Use Debian packaged libraries
 +.PHONY: clean
 --- a/src/utils/bedFile/Makefile
 +++ b/src/utils/bedFile/Makefile
-@@ -5,7 +5,6 @@ UTILITIES_DIR = ../../utils/
+@@ -5,7 +5,6 @@
  # define our includes
  # -------------------
  INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
@@ -215,7 +215,7 @@ Description: Use Debian packaged libraries
             -I$(UTILITIES_DIR)/fileType/ \
             -I$(UTILITIES_DIR)/stringUtilities/
  
-@@ -14,7 +13,7 @@ INCLUDES = -I$(UTILITIES_DIR)/lineFileUt
+@@ -14,7 +13,7 @@
  # ----------------------------------
  SOURCES= bedFile.cpp bedFile.h
  OBJECTS= $(SOURCES:.cpp=.o)
@@ -224,7 +224,7 @@ Description: Use Debian packaged libraries
  EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
  BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
  
-@@ -29,4 +28,4 @@ clean:
+@@ -29,4 +28,4 @@
  	@echo "Cleaning up."
  	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
  
@@ -233,7 +233,7 @@ Description: Use Debian packaged libraries
 +.PHONY: clean
 --- a/src/utils/bedGraphFile/Makefile
 +++ b/src/utils/bedGraphFile/Makefile
-@@ -13,7 +13,7 @@ INCLUDES =  -I$(UTILITIES_DIR)/lineFileU
+@@ -13,7 +13,7 @@
  # ----------------------------------
  SOURCES= bedGraphFile.cpp bedGraphFile.h
  OBJECTS= $(SOURCES:.cpp=.o)
@@ -244,7 +244,7 @@ Description: Use Debian packaged libraries
  
 --- a/src/utils/tabFile/Makefile
 +++ b/src/utils/tabFile/Makefile
-@@ -5,7 +5,6 @@ UTILITIES_DIR = ../../utils/
+@@ -5,7 +5,6 @@
  # define our includes
  # -------------------
  INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
@@ -252,7 +252,7 @@ Description: Use Debian packaged libraries
             -I$(UTILITIES_DIR)/fileType/
  
  # ----------------------------------
-@@ -13,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/lineFileUt
+@@ -13,7 +12,7 @@
  # ----------------------------------
  SOURCES= tabFile.cpp tabFile.h
  OBJECTS= $(SOURCES:.cpp=.o)
@@ -261,7 +261,7 @@ Description: Use Debian packaged libraries
  EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
  BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
  
-@@ -28,4 +27,4 @@ clean:
+@@ -28,4 +27,4 @@
  	@echo "Cleaning up."
  	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
  


=====================================
debian/rules
=====================================
@@ -17,6 +17,8 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 #endif
 
 override_dh_install:
+	cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam
+	cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam
 	dh_install
 	rm debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config
 


=====================================
src/filter/filter.c
=====================================
@@ -375,4 +375,5 @@ int main(int argc, char **argv)
     if(ret < -1) {
         errx(1, "lumpy_filter: error reading bam: %s\n", bam_file_name);
     }
+    return 0;
 }


=====================================
src/lumpy/SV_Pair.cpp
=====================================
@@ -52,6 +52,8 @@ SV_Pair(const BamAlignment &bam_a,
     else
         min_mapping_quality = bam_b.MapQuality;
 
+    read_id = bam_a.Name;
+
     struct interval tmp_a, tmp_b;
     tmp_a.start = bam_a.Position;
     tmp_a.end = bam_a.GetEndPosition(false, false) - 1;
@@ -341,6 +343,7 @@ void
 SV_Pair::
 print_evidence()
 {
+    cout << read_id << "\t";
     print_bedpe(0);
 }
 //}}}


=====================================
src/lumpy/SV_Pair.h
=====================================
@@ -61,6 +61,7 @@ class SV_Pair: public SV_Evidence
 		struct interval read_r;
 		bool read_l_is_split, read_r_is_split;
 		SV_PairReader *reader;
+		std::string read_id;
 
 
 		SV_Pair(const BamAlignment &bam_a,



View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/88089d9b9f787f708ef8eb5cad167250bae4e145...152e14e3eb24d40d5d4b83a372ab161b243e45ca

-- 
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/88089d9b9f787f708ef8eb5cad167250bae4e145...152e14e3eb24d40d5d4b83a372ab161b243e45ca
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