From d0af3648d1a981058cd414452089013be0ced73c Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 16 Sep 2014 10:16:45 -0400 Subject: [PATCH 1/2] Fixed a typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 58322d4..3472e91 100644 --- a/README.md +++ b/README.md @@ -87,7 +87,7 @@ settings: * Illumina paired-end reads no longer than ~70bp: bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai - bwa samsp ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam + bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam * PacBio subreads to a reference genome: From 230cd16712eab3ce07d231c39990aba8b59603fe Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 16 Sep 2014 10:17:30 -0400 Subject: [PATCH 2/2] updated dependency --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 60c2104..9bccbf6 100644 --- a/Makefile +++ b/Makefile @@ -40,7 +40,7 @@ depend: QSufSort.o: QSufSort.h bamlite.o: bamlite.h malloc_wrap.h -bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h +bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kseq.h bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h bwamem.o: ksort.h utils.h kbtree.h @@ -66,6 +66,7 @@ bwtsw2_core.o: khash.h ksort.h bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h bwtsw2_pair.o: malloc_wrap.h ksw.h +cutvar.o: bwa.h bntseq.h bwt.h kvec.h malloc_wrap.h example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h is.o: malloc_wrap.h @@ -75,5 +76,4 @@ ksw.o: ksw.h malloc_wrap.h main.o: kstring.h malloc_wrap.h utils.h malloc_wrap.o: malloc_wrap.h pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h -test-extend.o: ksw.h utils.o: utils.h ksort.h malloc_wrap.h kseq.h