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Imported from my local bwa repository, the master repository.

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1 parent 58628ff commit 007c3eb75d8ba6fb07131226b7f9081090dced54 Heng Li committed Jan 14, 2011
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  1. +674 −0 COPYING
  2. +3,815 −0 ChangeLog
  3. +55 −0 Makefile
  4. +528 −0 NEWS
  5. +155 −0 bamlite.c
  6. +94 −0 bamlite.h
  7. +303 −0 bntseq.c
  8. +80 −0 bntseq.h
  9. +550 −0 bwa.1
  10. +795 −0 bwape.c
  11. +677 −0 bwase.c
  12. +27 −0 bwase.h
  13. +198 −0 bwaseqio.c
  14. +250 −0 bwt.c
  15. +105 −0 bwt.h
  16. +23 −0 bwt_gen/Makefile
  17. +496 −0 bwt_gen/QSufSort.c
  18. +40 −0 bwt_gen/QSufSort.h
  19. +1,547 −0 bwt_gen/bwt_gen.c
  20. +105 −0 bwt_gen/bwt_gen.h
  21. +94 −0 bwt_lite.c
  22. +29 −0 bwt_lite.h
  23. +339 −0 bwtaln.c
  24. +147 −0 bwtaln.h
  25. +264 −0 bwtgap.c
  26. +38 −0 bwtgap.h
  27. +186 −0 bwtindex.c
  28. +77 −0 bwtio.c
  29. +267 −0 bwtmisc.c
  30. +51 −0 bwtsw2.h
  31. +650 −0 bwtsw2_aux.c
  32. +107 −0 bwtsw2_chain.c
  33. +594 −0 bwtsw2_core.c
  34. +93 −0 bwtsw2_main.c
  35. +191 −0 cs2nt.c
  36. +218 −0 is.c
  37. +506 −0 khash.h
  38. +208 −0 kseq.h
  39. +269 −0 ksort.h
  40. +35 −0 kstring.c
  41. +46 −0 kstring.h
  42. +90 −0 kvec.h
  43. +58 −0 main.c
  44. +29 −0 main.h
  45. +27 −0 qualfa2fq.pl
  46. +162 −0 simple_dp.c
  47. +111 −0 solid2fastq.pl
  48. +1,072 −0 stdaln.c
  49. +162 −0 stdaln.h
  50. +72 −0 utils.c
  51. +52 −0 utils.h
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3,815 ChangeLog

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@@ -0,0 +1,55 @@
+CC= gcc
+CXX= g++
+CFLAGS= -g -Wall -O2
+CXXFLAGS= $(CFLAGS)
+DFLAGS= -DHAVE_PTHREAD #-D_FILE_OFFSET_BITS=64
+OBJS= utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o \
+ bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o \
+ bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
+ bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
+ bwtsw2_chain.o bamlite.o
+PROG= bwa
+INCLUDES=
+LIBS= -lm -lz -lpthread -Lbwt_gen -lbwtgen
+SUBDIRS= . bwt_gen
+
+.SUFFIXES:.c .o .cc
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+.cc.o:
+ $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+lib-recur all-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)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+
+lib:
+
+bwa:lib-recur $(OBJS) main.o
+ $(CC) $(CFLAGS) $(DFLAGS) $(OBJS) main.o -o $@ $(LIBS)
+
+bwt.o:bwt.h
+bwtio.o:bwt.h
+bwtaln.o:bwt.h bwtaln.h kseq.h
+bwt1away.o:bwt.h bwtaln.h
+bwt2fmv.o:bwt.h
+bntseq.o:bntseq.h
+bwtgap.o:bwtgap.h bwtaln.h bwt.h
+
+bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
+bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
+bwtsw2_main.o:bwtsw2.h
+
+cleanlocal:
+ rm -f gmon.out *.o a.out $(PROG) *~ *.a
+
+clean:cleanlocal-recur
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