switch to bamkit

hall-lab · Feb 14, 2015 · 9a0b7f3 · 9a0b7f3
1 parent a28d313
commit 9a0b7f3
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Showing 10 changed files with 17 additions and 714 deletions.
diff --git a/.gitignore b/.gitignore
@@ -67,6 +67,7 @@ bin/lumpyToBedpe
 bin/bamgroupreads.py
 bin/bamfilterrg.py
 bin/bamcleanheader.py
+bin/bamlibs.py
 
 # Compiled source #
 ###################

diff --git a/.gitmodules b/.gitmodules
@@ -22,3 +22,6 @@
 [submodule "src/bwa"]
 	path = src/bwa
 	url = https://github.com/lh3/bwa.git
+[submodule "src/bamkit"]
+	path = src/bamkit
+	url = https://github.com/cc2qe/bamkit.git
diff --git a/Makefile b/Makefile
@@ -14,9 +14,9 @@ TABIX_DIR=$(SRC)/tabix
 VAWK_DIR=$(SRC)/vawk
 SVTOOLS_DIR=$(SRC)/svtools
 MBUFFER_DIR=$(SRC)/mbuffer
-SCRIPTS_DIR=$(SRC)/scripts
+BAMKIT_DIR=$(SRC)/bamkit
 
-all:	bwa sambamba samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer scripts cnvnator-multi
+all:	bwa sambamba samblaster freebayes lumpy svtyper tabix vawk svtools mbuffer bamkit cnvnator-multi
 
 bwa:
 	$(MAKE) -C $(BWA_DIR)
@@ -74,18 +74,20 @@ mbuffer:
 	$(MAKE) -C $(MBUFFER_DIR)
 	cp $(MBUFFER_DIR)/mbuffer $(TARGET_BIN)
 
-scripts:
-	cp $(SCRIPTS_DIR)/bamtofastq.py $(TARGET_BIN)
-	cp $(SCRIPTS_DIR)/bamheadrg.py $(TARGET_BIN)
-	cp $(SCRIPTS_DIR)/bamgroupreads.py $(TARGET_BIN)
-	cp $(SCRIPTS_DIR)/bamfilterrg.py $(TARGET_BIN)
-	cp $(SCRIPTS_DIR)/bamcleanheader.py $(TARGET_BIN)
+bamkit:
+	cp $(BAMKIT_DIR)/bamtofastq.py $(TARGET_BIN)
+	cp $(BAMKIT_DIR)/bamheadrg.py $(TARGET_BIN)
+	cp $(BAMKIT_DIR)/bamgroupreads.py $(TARGET_BIN)
+	cp $(BAMKIT_DIR)/bamfilterrg.py $(TARGET_BIN)
+	cp $(BAMKIT_DIR)/bamcleanheader.py $(TARGET_BIN)
+	cp $(BAMKIT_DIR)/bamlibs.py $(TARGET_BIN)
 
 clean:
 	rm -f \
 		bin/bedpeToBed12 \
 		bin/bedpeToVcf \
 		bin/bgzip \
+		bin/sambamba \
 		bin/cnvnator \
 		bin/cnvnator2VCF.pl \
 		bin/cnvnator_wrapper.py \
@@ -107,6 +109,7 @@ clean:
 		bin/bamgroupreads.py \
 		bin/bamfilterrg.py \
 		bin/bamcleanheader.py \
+		bin/bamlibs.py \
 		bin/cnvnator-multi \
 		bin/annotate_rd.py
 	$(MAKE) -C $(BWA_DIR) clean

diff --git a/bin/speedseq.config b/bin/speedseq.config
@@ -31,6 +31,7 @@ LUMPYTOBEDPE=$SPEEDSEQ_HOME/bin/lumpyToBedpe
 SVTYPER=$SPEEDSEQ_HOME/bin/svtyper
 BAMGROUPREADS=$SPEEDSEQ_HOME/bin/bamgroupreads.py
 BAMFILTERRG=$SPEEDSEQ_HOME/bin/bamfilterrg.py
+BAMLIBS=$SPEEDSEQ_HOME/bin/bamlibs.py
 
 # CNVnator 
 CNVNATOR_WRAPPER=$SPEEDSEQ_HOME/bin/cnvnator_wrapper.py

diff --git a/src/bamkit b/src/bamkit
diff --git a/src/scripts/bamcleanheader.py b/src/scripts/bamcleanheader.py
diff --git a/src/scripts/bamfilterrg.py b/src/scripts/bamfilterrg.py