pod5 vbz integration

Makefile

@@ -7,7 +7,13 @@ CC			= cc
 AR			= ar
 SVB			= thirdparty/streamvbyte
 SVBLIB		= $(SVB)/libstreamvbyte.a
-CPPFLAGS	+= -I include/ -I $(SVB)/include/
+# location of the modified vbz programs
+# clone the fork of pod5-file-format to thirdparty/pod5-file-format
+# git clone https://github.com/sashajenner/pod5-file-format thirdparty/pod5-file-format
+# cd thirdparty/pod5-file-format
+# git checkout svb16_clean
+VBZ		= thirdparty/pod5-file-format/c++/pod5_format
+CPPFLAGS	+= -I include/ -I $(SVB)/include/ -I $(VBZ)
 CFLAGS		+= -g -Wall -O2 -std=c99
 LDFLAGS		+= -lm -lz
 ifeq ($(zstd),1)
@@ -34,6 +40,7 @@ OBJ = $(BUILD_DIR)/slow5.o \
 		$(BUILD_DIR)/slow5_misc.o \
 		$(BUILD_DIR)/slow5_press.o \
 		$(BUILD_DIR)/slow5_mt.o \
+		$(VBZ)/signal_compression.o
 
 PREFIX = /usr/local
 VERSION = `git describe --tags`
@@ -55,6 +62,9 @@ $(SHAREDLIB): $(OBJ) $(SVBLIB)
 $(SVBLIB):
 	make -C $(SVB) no_simd=$(no_simd) libstreamvbyte.a
 
+$(VBZ)/signal_compression.o:
+	make -C $(VBZ) NO_SIMD=$(no_simd) ZSTD=$(zstd)
+
 $(BUILD_DIR)/slow5.o: src/slow5.c src/slow5_extra.h src/slow5_idx.h src/slow5_misc.h src/klib/ksort.h $(SLOW5_H)
 	$(CC) $(CFLAGS) $(CPPFLAGS) $< -c -fpic -o $@
 
@@ -73,6 +83,7 @@ $(BUILD_DIR)/slow5_mt.o: src/slow5_mt.c include/slow5/slow5_mt.h $(SLOW5_H)
 clean:
 	rm -rf $(OBJ) $(STATICLIB) $(SHAREDLIB) $(SHAREDLIBV)
 	make -C $(SVB) clean
+	make -C $(VBZ) clean
 
 # Delete all gitignored files (but not directories)
 distclean: clean

README.md

@@ -41,7 +41,11 @@ To build the C/C++ library :
 ```sh
 sudo apt-get install zlib1g-dev   #install zlib development libraries
 git clone https://github.com/hasindu2008/slow5lib
-cd slow5lib
+cd slow5lib/thirdparty
+git clone https://github.com/sashajenner/pod5-file-format
+cd pod5-file-format
+git checkout svb16_clean
+cd ../../
 make
 ```
 

include/slow5/slow5_press.h

@@ -61,8 +61,11 @@ extern "C" {
 enum slow5_press_method {
     SLOW5_COMPRESS_NONE,
     SLOW5_COMPRESS_ZLIB,
-    SLOW5_COMPRESS_SVB_ZD, /* streamvbyte zigzag delta */
+    SLOW5_COMPRESS_SVB_ZD,	/* 32-bit streamvbyte zigzag delta */
     SLOW5_COMPRESS_ZSTD,
+    SLOW5_COMPRESS_VBZ,		/* nanopore's pod5 vbz */
+    SLOW5_COMPRESS_SVB16_ZD,	/* vbz without zstd, aka 16-bit streamvbyte
+				   zigzag delta */
 };
 typedef struct{
     enum slow5_press_method record_method;