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initial commit, tabix 0.2.5

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ekg committed May 18, 2011
0 parents commit 645fdb21d8278502ff78e84c6d0b3095a84d9508
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  1. +593 −0 ChangeLog
  2. +63 −0 Makefile
  3. +126 −0 NEWS
  4. +395 −0 TabixReader.java
  5. +42 −0 bam_endian.h
  6. +156 −0 bedidx.c
  7. +714 −0 bgzf.c
  8. +157 −0 bgzf.h
  9. +206 −0 bgzip.c
  10. BIN example.gtf.gz
  11. BIN example.gtf.gz.tbi
  12. +998 −0 index.c
  13. +486 −0 khash.h
  14. +632 −0 knetfile.c
  15. +75 −0 knetfile.h
  16. +227 −0 kseq.h
  17. +271 −0 ksort.h
  18. +165 −0 kstring.c
  19. +68 −0 kstring.h
  20. +290 −0 main.c
  21. +8 −0 perl/MANIFEST
  22. +8 −0 perl/Makefile.PL
  23. +76 −0 perl/Tabix.pm
  24. +71 −0 perl/Tabix.xs
  25. +41 −0 perl/TabixIterator.pm
  26. +28 −0 perl/t/01local.t
  27. +28 −0 perl/t/02remote.t
  28. +3 −0 perl/typemap
  29. +55 −0 python/setup.py
  30. +408 −0 python/tabixmodule.c
  31. +91 −0 python/test.py
  32. +132 −0 tabix.1
  33. +145 −0 tabix.h
  34. +87 −0 tabix.py
  35. +121 −0 tabix.tex
593 ChangeLog

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+CC= gcc
+CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppc
+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+LOBJS= bgzf.o kstring.o knetfile.o index.o bedidx.o
+AOBJS= main.o
+PROG= tabix bgzip
+INCLUDES=
+SUBDIRS= .
+LIBPATH=
+LIBCURSES=
+
+.SUFFIXES:.c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+ @target=`echo $@ | sed s/-recur//`; \
+ wdir=`pwd`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ cd $$subdir; \
+ $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+
+all:$(PROG)
+
+lib:libtabix.a
+
+libtabix.so.1:$(LOBJS)
+ $(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
+
+libtabix.1.dylib:$(LOBJS)
+ libtool -dynamic $(LOBJS) -o $@ -lc -lz
+
+libtabix.a:$(LOBJS)
+ $(AR) -cru $@ $(LOBJS)
+
+tabix:lib $(AOBJS)
+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
+
+bgzip:bgzip.o bgzf.o knetfile.o
+ $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+
+TabixReader.class:TabixReader.java
+ javac -cp .:sam.jar TabixReader.java
+
+kstring.o:kstring.h
+knetfile.o:knetfile.h
+bgzf.o:bgzf.h knetfile.h
+index.o:bgzf.h tabix.h khash.h ksort.h kstring.h
+main.o:tabix.h kstring.h bgzf.h
+bgzip.o:bgzf.h
+bedidx.o:kseq.h khash.h
+
+tabix.pdf:tabix.tex
+ pdflatex tabix.tex
+
+cleanlocal:
+ rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log tabix.pdf *.class libtabix.*.dylib libtabix.so*
+
+clean:cleanlocal-recur
126 NEWS
@@ -0,0 +1,126 @@
+Release 0.2.4 (10 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Give an error if the index file is older than the data file.
+
+ * Avoid a segfault given flawed input.
+
+ * Added Python APIs contributed by Hyeshik Chang. The new APIs do not bind to
+ the dynamic library and are reported to be faster. Pysam also comes with a
+ tabix binding.
+
+ * Added option "-r" for efficient header replacement.
+
+ * Added BED support.
+
+ * Synchronized the BGZF library between tabix and samtools.
+
+(0.2.4: 10 April 2011, r949)
+
+
+
+Beta Release 0.2.3 (8 December, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Fixed a minor bug where the first record in a headerless file may be
+ missed.
+
+ * Added an option to print header lines.
+
+ * Fixed a rare bug which may occasionally happen when retrieving data
+ from a region without any records.
+
+ * Enhanced error reporting.
+
+ * Fixed a bug in bgzip which may delete the original file even if not
+ intended.
+
+(0.2.3: 8 December 2010, r876)
+
+
+
+Beta Release 0.2.2 (28 June, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Dropped the VCF3 support. Added VCF4 support.
+
+ * Avoided the function name collision with samtools.
+
+(0.2.2: 28 June 2010, r603)
+
+
+
+Beta Release 0.2.1 (3 June, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Allow shared library to be compiled. Added python binding to the
+ shared library.
+
+(0.2.1: 3 June 2010, r582)
+
+
+
+Beta Release 0.2.0 (11 May, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Fixed an issue for random access given an interval end larger than
+ 2^29.
+
+ * Updated the Java binding.
+
+ * Added a Perl module using XS.
+
+ * Improved the C APIs.
+
+(0.2.0: 11 May 2010, r574)
+
+
+
+Beta Release 0.1.6 (9 May, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Improved backward compatibility. Release 0.1.5 does not work with the
+ buggy index file generated by 0.1.2.
+
+ * Fixed a bug in building linear index. The bug does not affect the
+ results, only affects efficiency in rare cases.
+
+ * Reduced the number of seek calls given an index generated by old
+ version of tabix.
+
+ * Added new APIs for retrieving data via an iterator. The old callback
+ APIs are not changed, although internally it uses iterator to
+ retrieve data.
+
+I am trying to freeze tabix. I just hope I am committing new bugs.
+
+(0.1.6: 9 May 2010, r563)
+
+
+
+Beta Release 0.1.5 (5 May, 2010)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Notable changes:
+
+ * Clarified that tabix is released under MIT/X11.
+
+ * Improved the robustness of indexing and retrieval.
+
+ * Reduced the number of seek calls when the specified region starts
+ from a 16kb block with no data. The index format is the same, but the
+ content is changed a little.
+
+(0.1.5: 5 May 2010, r560)
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