From: Heng Li <lh3@live.co.uk>
Date: Tue, 28 Apr 2009 12:10:23 +0000 (+0000)
Subject: * samtools-0.1.3-7 (r246)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=41586185b43962c1ffb3f82e93066a480254aa17;p=samtools.git
* samtools-0.1.3-7 (r246)
* incorporated revisions from Nils Homer
* enhanced support of displaying color-space reads
---
diff --git a/ChangeLog b/ChangeLog
index e2958e7..a096816 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,104 @@
+------------------------------------------------------------------------
+r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-6 (r244)
+ * fixed segfault for unmapped reads
+
+------------------------------------------------------------------------
+r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-5 (r243)
+ * fixed a long existing bug which may cause memory leak
+ * check MD
+ * consensus calling now works with "=", but indel calling not
+
+------------------------------------------------------------------------
+r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-4 (r242)
+ * fixed a memory leak
+
+------------------------------------------------------------------------
+r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.lite
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ A /trunk/samtools/bam_md.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-3 (r240)
+ * generate MD tag
+ * generate "=" bases
+ * the plain pileup now support "=" bases, but consensus calling and glfgen may fail
+
+------------------------------------------------------------------------
+r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-2 (r239)
+ * fixed bugs in bam_aux.c (these functions nevered used by samtools)
+ * removed bam_aux_init()/bam_aux_destroy()
+ * added tagview for testing bam_aux
+
+------------------------------------------------------------------------
+r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-1
+ * fixed a bug in pileup: the first read in a chromosome may not be printed
+
+------------------------------------------------------------------------
+r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.lite
+
+a missing file in Makefile.lite
+
+------------------------------------------------------------------------
+r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.3
+
+------------------------------------------------------------------------
+r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-28
+ * make samtools more robust to weird input such as empty file
+
+------------------------------------------------------------------------
+r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/samtools.1
+
+prepare for release 0.1.3
+
------------------------------------------------------------------------
r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 25897db..0000000
--- a/Makefile
+++ /dev/null
@@ -1,65 +0,0 @@
-CC= gcc
-CXX= g++
-CFLAGS= -g -Wall -O2 -m64 #-arch ppc
-CXXFLAGS= $(CFLAGS)
-DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
-OBJS= bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
- razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
- bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o
-PROG= razip bgzip samtools
-INCLUDES=
-LIBS= -lm -lz
-SUBDIRS= . misc
-
-.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)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
- INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
- cd $$wdir; \
- done;
-
-all:$(PROG)
-
-lib:libbam.a
-
-libbam.a:$(OBJS)
- $(AR) -cru $@ $(OBJS)
-
-samtools:lib bamtk.o
- $(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
-
-razip:razip.o razf.o
- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
-
-bgzip:bgzip.o bgzf.o
- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
-
-razip.o:razf.h
-bam.o:bam.h razf.h bam_endian.h
-bam_import.o:bam.h kseq.h khash.h razf.h
-bam_pileup.o:bam.h razf.h ksort.h
-bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
-bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
-bam_lpileup.o:bam.h ksort.h
-bam_tview.o:bam.h faidx.h bam_maqcns.h
-bam_maqcns.o:bam.h ksort.h bam_maqcns.h
-bam_sort.o:bam.h ksort.h razf.h
-bam_md.o:bam.h faidx.h
-razf.o:razf.h
-glf.o:glf.h
-
-faidx.o:faidx.h razf.h khash.h
-faidx_main.o:faidx.h razf.h
-
-cleanlocal:
- rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
-
-clean:cleanlocal-recur
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..e2304f7
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,56 @@
+EXTRA_DIST = autogen.sh
+bin_PROGRAMS = bgzip samtools razip
+SUBDIRS = . misc
+
+bgzip_SOURCES = bgzip.c bgzf.c
+bgzip_LDADD = -lm -lz
+
+samtools_SOURCES = bamtk.c bam.c bam_aux.c bam_import.c bam_index.c \
+ bam_lpileup.c bam_maqcns.c bam_mate.c bam_md.c bam_pileup.c \
+ bam_plcmd.c bam_rmdup.c bam_sort.c bam_stat.c \
+ bam_tview.c bgzf.c faidx.c glf.c kstring.c razf.c \
+ bam.h bam_endian.h bam_maqcns.h bgzf.h faidx.h glf.h \
+ khash.h kseq.h kstring.h ksort.h razf.h zutil.h
+samtools_LDADD = -lm -lz -lcurses
+
+razip_SOURCES = razip.c razf.c
+razip_LDADD = -lm -lz
+dist_bin_SCRIPTS = bowtie2sam.pl export2sam.pl novo2sam.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
+bin_PROGRAMS = faidx maq2sam-short maq2sam-long md5fa md5sum-lite wgsim
+
+faidx_SOURCES = ../faidx.c ../faidx.c
+#faidx_LDFLAGS = -D_NO_RAZF -DFAIDX_MAIN
+
+md5fa_SOURCES = md5.c md5.h md5fa.c ../kseq.h
+#md5fa_LDADD = -lz
+
+md5sum_lite_SOURCES = md5.c md5.h
+#md5sum_lite_LDFLAGS = -DMD5SUM_MAIN
+
+maq2sam_short_SOURCES = maq2sam.c
+#maq2sam_short_LDADD = -lz
+
+maq2sam_long_SOURCES = maq2sam.c
+#maq2sam_long_LDADD = -lz
+
+wgsim_SOURCES = wgsim.c
+wgsim_LDADD = -lm
+
+faidx:../faidx.c ../faidx.h
+ $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+md5fa:md5.o md5fa.o md5.h ../kseq.h
+ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+md5fa.o:md5.h md5fa.c
+ $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+md5sum-lite:md5sum-lite.o
+ $(CC) $(CFLAGS) -o $@ md5sum-lite.o
+md5sum-lite.o:md5.c md5.h
+ $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+maq2sam-short:maq2sam-short.o
+ $(CC) $(CFLAGS) -o $@ maq2sam-short.o -lz
+maq2sam-short.o:maq2sam.c
+ $(CC) -c $(CFLAGS) -o $@ maq2sam.c
+maq2sam-long:maq2sam-long.o
+ $(CC) $(CFLAGS) -o $@ maq2sam-long.o -lz
+maq2sam-long.o:maq2sam.c
+ $(CC) -c $(CFLAGS) -DMAQ_LONGREADS -D_MAQ_LONGREADS -o $@ maq2sam.c
diff --git a/Makefile.generic b/Makefile.generic
new file mode 100644
index 0000000..002c71a
--- /dev/null
+++ b/Makefile.generic
@@ -0,0 +1,65 @@
+CC= gcc
+CXX= g++
+CFLAGS= -g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS= $(CFLAGS)
+DFLAGS= -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+OBJS= bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
+ razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
+ bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o
+PROG= razip bgzip samtools
+INCLUDES=
+LIBS= -lm -lz
+SUBDIRS= . misc
+
+.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; \
+ $(MAKE) -f Makefile.generic CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+ INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \
+ cd $$wdir; \
+ done;
+
+all:$(PROG)
+
+lib:libbam.a
+
+libbam.a:$(OBJS)
+ $(AR) -cru $@ $(OBJS)
+
+samtools:lib bamtk.o
+ $(CC) $(CFLAGS) -o $@ bamtk.o $(LIBS) -L. -lbam -lcurses
+
+razip:razip.o razf.o
+ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(LIBS)
+
+bgzip:bgzip.o bgzf.o
+ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(LIBS)
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h bam_maqcns.h
+bam_maqcns.o:bam.h ksort.h bam_maqcns.h
+bam_sort.o:bam.h ksort.h razf.h
+bam_md.o:bam.h faidx.h
+razf.o:razf.h
+glf.o:glf.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+cleanlocal:
+ rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur
diff --git a/autogen.sh b/autogen.sh
new file mode 100644
index 0000000..99f0a5f
--- /dev/null
+++ b/autogen.sh
@@ -0,0 +1,51 @@
+#!/bin/sh
+
+run ()
+{
+ echo "running: $*"
+ eval $*
+
+ if test $? != 0 ; then
+ echo "error: while running '$*'"
+ exit 1
+ fi
+}
+
+run aclocal
+run autoheader
+run automake -a
+run autoconf
+#!/bin/sh
+
+run ()
+{
+ echo "running: $*"
+ eval $*
+
+ if test $? != 0 ; then
+ echo "error: while running '$*'"
+ exit 1
+ fi
+}
+
+run aclocal
+run autoheader
+run automake -a
+run autoconf
+#!/bin/sh
+
+run ()
+{
+ echo "running: $*"
+ eval $*
+
+ if test $? != 0 ; then
+ echo "error: while running '$*'"
+ exit 1
+ fi
+}
+
+run aclocal
+run autoheader
+run automake -a
+run autoconf
diff --git a/bam.h b/bam.h
index b607f96..4045684 100644
--- a/bam.h
+++ b/bam.h
@@ -606,6 +606,35 @@ extern "C" {
char bam_aux2A(const uint8_t *s);
char *bam_aux2Z(const uint8_t *s);
+ /*!
+ @abstract Get the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCSi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color quality of the color encoding the previous and current base
+ @param b pointer to an alignment
+ @param i The i-th position, 0-based
+ @return color quality
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCQi(bam1_t *b, int i);
+
+ /*!
+ @abstract Get the color error profile at the give position
+ @param b pointer to an alignment
+ @return the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion Returns 0 no color information is found.
+ */
+ char bam_aux_getCEi(bam1_t *b, int i);
+
/*!
@abstract Calculate the rightmost coordinate of an alignment on the
reference genome.
diff --git a/bam_aux.c b/bam_aux.c
index d6f18ea..2fa9ac2 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -74,7 +74,7 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
bam_init_header_hash(header);
h = (khash_t(s)*)header->hash;
-
+
l = strlen(str);
p = s = (char*)malloc(l+1);
/* squeeze out "," */
@@ -152,3 +152,105 @@ char *bam_aux2Z(const uint8_t *s)
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
+
+char bam_aux_getCSi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) i = strlen(cs) - 1 - i;
+ else i++;
+ return cs[i];
+}
+
+char bam_aux_getCQi(bam1_t *b, int i)
+{
+ uint8_t *c = bam_aux_get(b, "CQ");
+ char *cq = NULL;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cq = bam_aux2Z(c);
+ // adjust for strandedness
+ if(bam1_strand(b)) i = strlen(cq) - 1 - i;
+ return cq[i];
+}
+
+char bam_aux_nt2int(char a)
+{
+ switch(toupper(a)) {
+ case 'A':
+ return 0;
+ break;
+ case 'C':
+ return 1;
+ break;
+ case 'G':
+ return 2;
+ break;
+ case 'T':
+ return 3;
+ break;
+ default:
+ return 4;
+ break;
+ }
+}
+
+char bam_aux_ntnt2cs(char a, char b)
+{
+ a = bam_aux_nt2int(a);
+ b = bam_aux_nt2int(b);
+ if(4 == a || 4 == b) return '4';
+ return "0123"[(int)(a ^ b)];
+}
+
+char bam_aux_getCEi(bam1_t *b, int i)
+{
+ int cs_i;
+ uint8_t *c = bam_aux_get(b, "CS");
+ char *cs = NULL;
+ char prev_b, cur_b;
+ char cur_color, cor_color;
+
+ // return the base if the tag was not found
+ if(0 == c) return 0;
+
+ cs = bam_aux2Z(c);
+
+ // adjust for strandedness and leading adaptor
+ if(bam1_strand(b)) { //reverse strand
+ cs_i = strlen(cs) - 1 - i;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base
+ prev_b = (0 == cs_i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+ else {
+ cs_i=i+1;
+ // get current color
+ cur_color = cs[cs_i];
+ // get previous base
+ prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
+ // get current base
+ cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
+ }
+
+ // corrected color
+ cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
+
+ if(cur_color == cor_color) {
+ return '-';
+ }
+ else {
+ return cur_color;
+ }
+}
diff --git a/bam_tview.c b/bam_tview.c
index 77d60a0..c6780c3 100644
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -11,9 +11,14 @@
#define TV_MAX_GOTO 40
#define TV_LOW_MAPQ 10
-#define TV_COLOR_MAPQ 0
-#define TV_COLOR_BASEQ 1
-#define TV_COLOR_NUCL 2
+#define TV_COLOR_MAPQ 0
+#define TV_COLOR_BASEQ 1
+#define TV_COLOR_NUCL 2
+#define TV_COLOR_COL 3
+#define TV_COLOR_COLQ 4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
typedef struct {
int mrow, mcol;
@@ -27,7 +32,7 @@ typedef struct {
faidx_t *fai;
bam_maqcns_t *bmc;
- int ccol, last_pos, row_shift, color_for, is_nucl, l_ref;
+ int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins;
char *ref;
} tview_t;
@@ -56,10 +61,12 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
attron(attr);
mvaddch(2, tv->ccol, c);
attroff(attr);
- // calculate maximum insert
- for (i = 0; i < n; ++i) {
- const bam_pileup1_t *p = pl + i;
- if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+ if(tv->ins) {
+ // calculate maximum insert
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
+ }
}
// core loop
for (j = 0; j <= max_ins; ++j) {
@@ -68,21 +75,35 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
int row = TV_MIN_ALNROW + p->level - tv->row_shift;
if (j == 0) {
if (!p->is_del) {
- c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
- if (!tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ if (tv->base_for == TV_BASE_COLOR_SPACE &&
+ (c = bam_aux_getCSi(p->b, p->qpos))) {
+ c = bam_aux_getCSi(p->b, p->qpos);
+ // assume that if we found one color, we will be able to get the color error
+ if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
+ }
+ else {
+ c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+ if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ }
} else c = '*';
} else { // padding
if (j > p->indel) c = '*';
else { // insertion
- c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
- if (j == 0 && !tv->is_nucl && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ if (tv->base_for == TV_BASE_NUCL) {
+ c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+ if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
+ }
+ else {
+ c = bam_aux_getCSi(p->b, p->qpos + j);
+ if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
+ }
}
}
if (row > TV_MIN_ALNROW && row < tv->mrow) {
int x;
attr = 0;
if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
- || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+ || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
if (tv->color_for == TV_COLOR_BASEQ) {
x = bam1_qual(p->b)[p->qpos]/10 + 1;
if (x > 4) x = 4;
@@ -94,6 +115,24 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
} else if (tv->color_for == TV_COLOR_NUCL) {
x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COL) {
+ x = 0;
+ switch(bam_aux_getCSi(p->b, p->qpos)) {
+ case '0': x = 0; break;
+ case '1': x = 1; break;
+ case '2': x = 2; break;
+ case '3': x = 3; break;
+ case '4': x = 4; break;
+ default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
+ }
+ x+=5;
+ attr |= COLOR_PAIR(x);
+ } else if(tv->color_for == TV_COLOR_COLQ) {
+ x = bam_aux_getCQi(p->b, p->qpos);
+ if(0 == x) x = bam1_qual(p->b)[p->qpos];
+ x = x/10 + 1;
+ if (x > 4) x = 4;
+ attr |= COLOR_PAIR(x);
}
attron(attr);
mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
@@ -122,20 +161,21 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
tv->bmc = bam_maqcns_init();
+ tv->ins = 1;
bam_maqcns_prepare(tv->bmc);
initscr();
keypad(stdscr, TRUE);
- clear();
- noecho();
- cbreak();
+ clear();
+ noecho();
+ cbreak();
#ifdef NCURSES_VERSION
getmaxyx(stdscr, tv->mrow, tv->mcol);
#else
tv->mrow = 80; tv->mcol = 40;
#endif
tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
- tv->whelp = newwin(22,40, 5, 5);
+ tv->whelp = newwin(27, 40, 5, 5);
tv->color_for = TV_COLOR_MAPQ;
start_color();
init_pair(1, COLOR_BLUE, COLOR_BLACK);
@@ -200,8 +240,8 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos)
char str[256];
int i, l = 0;
wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(tv->wgoto, 1, 2, "Goto: ");
- for (;;) {
+ mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+ for (;;) {
int c = wgetch(tv->wgoto);
wrefresh(tv->wgoto);
if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
@@ -220,35 +260,40 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos)
str[l] = '\0';
for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
mvwprintw(tv->wgoto, 1, 8, "%s", str);
- }
+ }
}
static void tv_win_help(tview_t *tv) {
- int r = 1;
+ int r = 1;
WINDOW *win = tv->whelp;
- wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(win, r++, 2, " -=- Help -=- ");
- r++;
- mvwprintw(win, r++, 2, "? This window");
- mvwprintw(win, r++, 2, "Arrows Small scroll movement");
- mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
- mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
- mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
- mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
- mvwprintw(win, r++, 2, "space Scroll one screen");
- mvwprintw(win, r++, 2, "backspace Scroll back one screen");
- mvwprintw(win, r++, 2, "g Go to specific location");
- mvwprintw(win, r++, 2, "b Color for base quality");
- mvwprintw(win, r++, 2, "m Color for mapping qual");
- mvwprintw(win, r++, 2, "n Color for nucleotide");
- mvwprintw(win, r++, 2, ". Toggle on/off dot view");
- mvwprintw(win, r++, 2, "q Exit");
+ wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(win, r++, 2, " -=- Help -=- ");
+ r++;
+ mvwprintw(win, r++, 2, "? This window");
+ mvwprintw(win, r++, 2, "Arrows Small scroll movement");
+ mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
+ mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
+ mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
+ mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
+ mvwprintw(win, r++, 2, "space Scroll one screen");
+ mvwprintw(win, r++, 2, "backspace Scroll back one screen");
+ mvwprintw(win, r++, 2, "g Go to specific location");
+ mvwprintw(win, r++, 2, "m Color for mapping qual");
+ mvwprintw(win, r++, 2, "n Color for nucleotide");
+ mvwprintw(win, r++, 2, "b Color for base quality");
+ mvwprintw(win, r++, 2, "c Color for cs color");
+ mvwprintw(win, r++, 2, "z Color for cs qual");
+ mvwprintw(win, r++, 2, ". Toggle on/off dot view");
+ mvwprintw(win, r++, 2, "N Turn on nt view");
+ mvwprintw(win, r++, 2, "C Turn on cs view");
+ mvwprintw(win, r++, 2, "i Toggle on/off ins");
+ mvwprintw(win, r++, 2, "q Exit");
r++;
mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
- wrefresh(win);
- wgetch(win);
+ wrefresh(win);
+ wgetch(win);
}
void tv_loop(tview_t *tv)
@@ -259,35 +304,40 @@ void tv_loop(tview_t *tv)
int c = getch();
if(256 < c) {c = 1 + (c%256);} // Terminal was displaying ctrl-H as 263 via ssh from Mac OS X 10.5 computer
switch (c) {
- case '?': tv_win_help(tv); break;
- case '\033':
- case 'q': goto end_loop;
- case 'g': tv_win_goto(tv, &tid, &pos); break;
- case 'b': tv->color_for = TV_COLOR_BASEQ; break;
- case 'm': tv->color_for = TV_COLOR_MAPQ; break;
- case 'n': tv->color_for = TV_COLOR_NUCL; break;
- case KEY_LEFT:
- case 'h': --pos; break;
- case KEY_RIGHT:
- case 'l': ++pos; break;
- case KEY_SLEFT:
- case 'H': pos -= 20; break;
- case KEY_SRIGHT:
- case 'L': pos += 20; break;
- case '.': tv->is_nucl = !tv->is_nucl; break;
- case '\010': pos -= 1000; break;
- case '\014': pos += 1000; break;
- case ' ': pos += tv->mcol; break;
- case KEY_UP:
- case 'j': --tv->row_shift; break;
- case KEY_DOWN:
- case 'k': ++tv->row_shift; break;
- case KEY_BACKSPACE:
- case '\177': pos -= tv->mcol; break;
+ case '?': tv_win_help(tv); break;
+ case '\033':
+ case 'q': goto end_loop;
+ case 'g': tv_win_goto(tv, &tid, &pos); break;
+ case 'm': tv->color_for = TV_COLOR_MAPQ; break;
+ case 'b': tv->color_for = TV_COLOR_BASEQ; break;
+ case 'n': tv->color_for = TV_COLOR_NUCL; break;
+ case 'c': tv->color_for = TV_COLOR_COL; break;
+ case 'z': tv->color_for = TV_COLOR_COLQ; break;
+ case KEY_LEFT:
+ case 'h': --pos; break;
+ case KEY_RIGHT:
+ case 'l': ++pos; break;
+ case KEY_SLEFT:
+ case 'H': pos -= 20; break;
+ case KEY_SRIGHT:
+ case 'L': pos += 20; break;
+ case '.': tv->is_dot = !tv->is_dot; break;
+ case 'N': tv->base_for = TV_BASE_NUCL; break;
+ case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+ case 'i': tv->ins = !tv->ins; break;
+ case '\010': pos -= 1000; break;
+ case '\014': pos += 1000; break;
+ case ' ': pos += tv->mcol; break;
+ case KEY_UP:
+ case 'j': --tv->row_shift; break;
+ case KEY_DOWN:
+ case 'k': ++tv->row_shift; break;
+ case KEY_BACKSPACE:
+ case '\177': pos -= tv->mcol; break;
#ifdef KEY_RESIZE
- case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+ case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
#endif
- default: continue;
+ default: continue;
}
if (pos < 0) pos = 0;
if (tv->row_shift < 0) tv->row_shift = 0;
diff --git a/bamtk.c b/bamtk.c
index aed8a39..ab39e9d 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-6 (r244)"
+#define PACKAGE_VERSION "0.1.3-7 (r246)"
#endif
int bam_taf2baf(int argc, char *argv[]);
diff --git a/cleanup.sh b/cleanup.sh
new file mode 100644
index 0000000..96381e6
--- /dev/null
+++ b/cleanup.sh
@@ -0,0 +1,12 @@
+if [ -f "Makefile" ]; then
+ make distclean
+fi
+rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs
+if [ -f "Makefile" ]; then
+ make distclean
+fi
+rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs
+if [ -f "Makefile" ]; then
+ make distclean
+fi
+rm -fr *~ .in .gdb_history Makefile.in aclocal.m4 configure autom4*.cache config.guess config.h.in config.sub depcomp install-sh missing mkinstalldirs
diff --git a/configure.ac b/configure.ac
new file mode 100644
index 0000000..7bd8696
--- /dev/null
+++ b/configure.ac
@@ -0,0 +1,108 @@
+AC_INIT(SAMTOOLS, 0.1.3)
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE([no-dependencies])
+AC_CANONICAL_HOST
+
+AC_PROG_INSTALL
+
+AC_PROG_CC
+AC_PROG_CXX
+
+# set CFLAGS and CXXFLAGS
+user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
+generic_CFLAGS="-Wall -L."
+
+AC_ARG_ENABLE(norazf, [ --disable-razf disable razf support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_RAZF"], [])
+AC_ARG_ENABLE(nocurses, [ --disable-curses disable curses support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_CURSES"], [])
+CFLAGS="${generic_CFLAGS} ${user_CFLAGS}"
+CXXFLAGS=$CFLAGS
+
+AC_STDC_HEADERS
+AC_CHECK_FUNCS([bzero memset pow sqrt strcasecmp strdup strstr strtol])
+AC_CHECK_HEADERS([zlib.h fcntl.h malloc.h stddef.h])
+AC_CHECK_TYPES([ptrdiff_t])
+AC_C_CONST
+AC_C_INLINE
+AC_FUNC_FSEEKO
+AC_FUNC_MALLOC
+AC_FUNC_MEMCMP
+AC_FUNC_REALLOC
+AC_HEADER_STDBOOL
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+
+AC_OUTPUT([Makefile misc/Makefile])
+AC_INIT(SAMTOOLS, 0.1.3)
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE([no-dependencies])
+AC_CANONICAL_HOST
+
+AC_PROG_INSTALL
+
+AC_PROG_CC
+AC_PROG_CXX
+
+# set CFLAGS and CXXFLAGS
+user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
+generic_CFLAGS="-Wall -L."
+
+AC_ARG_ENABLE(norazf, [ --disable-razf disable razf support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_RAZF"], [])
+AC_ARG_ENABLE(nocurses, [ --disable-curses disable curses support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_CURSES"], [])
+CFLAGS="${generic_CFLAGS} ${user_CFLAGS}"
+CXXFLAGS=$CFLAGS
+
+AC_STDC_HEADERS
+AC_CHECK_FUNCS([bzero memset pow sqrt strcasecmp strdup strstr strtol])
+AC_CHECK_HEADERS([zlib.h fcntl.h malloc.h stddef.h])
+AC_CHECK_TYPES([ptrdiff_t])
+AC_C_CONST
+AC_C_INLINE
+AC_FUNC_FSEEKO
+AC_FUNC_MALLOC
+AC_FUNC_MEMCMP
+AC_FUNC_REALLOC
+AC_HEADER_STDBOOL
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+
+AC_OUTPUT([Makefile misc/Makefile])
+AC_INIT(SAMTOOLS, 0.1.3)
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE([no-dependencies])
+AC_CANONICAL_HOST
+
+AC_PROG_INSTALL
+
+AC_PROG_CC
+AC_PROG_CXX
+
+# set CFLAGS and CXXFLAGS
+user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
+generic_CFLAGS="-Wall -L."
+
+AC_ARG_ENABLE(norazf, [ --disable-razf disable razf support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_RAZF"], [])
+AC_ARG_ENABLE(nocurses, [ --disable-curses disable curses support],
+ [user_DFLAGS="${user_DFLAGS} -D_NO_CURSES"], [])
+CFLAGS="${generic_CFLAGS} ${user_CFLAGS}"
+CXXFLAGS=$CFLAGS
+
+AC_STDC_HEADERS
+AC_CHECK_FUNCS([bzero memset pow sqrt strcasecmp strdup strstr strtol])
+AC_CHECK_HEADERS([zlib.h fcntl.h malloc.h stddef.h])
+AC_CHECK_TYPES([ptrdiff_t])
+AC_C_CONST
+AC_C_INLINE
+AC_FUNC_FSEEKO
+AC_FUNC_MALLOC
+AC_FUNC_MEMCMP
+AC_FUNC_REALLOC
+AC_HEADER_STDBOOL
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+
+AC_OUTPUT([Makefile misc/Makefile])
diff --git a/misc/Makefile b/misc/Makefile
deleted file mode 100644
index 0f65881..0000000
--- a/misc/Makefile
+++ /dev/null
@@ -1,58 +0,0 @@
-CC= gcc
-CXX= g++
-CFLAGS= -g -Wall -O2 -m64 #-arch ppc
-CXXFLAGS= $(CFLAGS)
-DFLAGS= #-D_FILE_OFFSET_BITS=64
-OBJS=
-PROG= faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
-INCLUDES= -I..
-LIBS= -lm -lz
-SUBDIRS= .
-
-.SUFFIXES:.c .o
-
-.c.o:
- $(CC) -c $(CFLAGS) $(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:
-
-wgsim:wgsim.o
- $(CC) $(CFLAGS) -o $@ wgsim.o -lm
-
-faidx:../faidx.c ../faidx.h
- $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-
-md5fa:md5.o md5fa.o md5.h ../kseq.h
- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-
-md5sum-lite:md5sum-lite.o
- $(CC) $(CFLAGS) -o $@ md5sum-lite.o
-
-md5sum-lite.o:md5.c md5.h
- $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
-
-maq2sam-short:maq2sam.c
- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
-
-maq2sam-long:maq2sam.c
- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
-
-md5fa.o:md5.h md5fa.c
- $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
-
-cleanlocal:
- rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
-
-clean:cleanlocal-recur
diff --git a/misc/Makefile.generic b/misc/Makefile.generic
new file mode 100644
index 0000000..0f65881
--- /dev/null
+++ b/misc/Makefile.generic
@@ -0,0 +1,58 @@
+CC= gcc
+CXX= g++
+CFLAGS= -g -Wall -O2 -m64 #-arch ppc
+CXXFLAGS= $(CFLAGS)
+DFLAGS= #-D_FILE_OFFSET_BITS=64
+OBJS=
+PROG= faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
+INCLUDES= -I..
+LIBS= -lm -lz
+SUBDIRS= .
+
+.SUFFIXES:.c .o
+
+.c.o:
+ $(CC) -c $(CFLAGS) $(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:
+
+wgsim:wgsim.o
+ $(CC) $(CFLAGS) -o $@ wgsim.o -lm
+
+faidx:../faidx.c ../faidx.h
+ $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+
+md5fa:md5.o md5fa.o md5.h ../kseq.h
+ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+
+md5sum-lite:md5sum-lite.o
+ $(CC) $(CFLAGS) -o $@ md5sum-lite.o
+
+md5sum-lite.o:md5.c md5.h
+ $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+
+maq2sam-short:maq2sam.c
+ $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
+
+maq2sam-long:maq2sam.c
+ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
+
+md5fa.o:md5.h md5fa.c
+ $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+
+cleanlocal:
+ rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+
+clean:cleanlocal-recur