第一次merge

.gitignore

@@ -5,3 +5,56 @@ test64
 .*.swp
 Makefile.bak
 bwamem-lite
+# ---> C
+# Prerequisites
+*.d
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.mod*
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf

README.md

@@ -184,3 +184,6 @@ run the post-processing script.
 [16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/
 [17]: http://sourceforge.net/projects/bio-bwa/files/bwakit/
 [18]: https://github.com/lh3/bwa/blob/master/README-alt.md
+# fast-bwa
+
+基于bwa，做一些优化，注释