From 41586185b43962c1ffb3f82e93066a480254aa17 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 28 Apr 2009 12:10:23 +0000 Subject: [PATCH] * samtools-0.1.3-7 (r246) * incorporated revisions from Nils Homer * enhanced support of displaying color-space reads --- ChangeLog | 101 +++++++++++++++ Makefile.am | 56 +++++++++ Makefile => Makefile.generic | 2 +- autogen.sh | 51 ++++++++ bam.h | 29 +++++ bam_aux.c | 104 +++++++++++++++- bam_tview.c | 184 ++++++++++++++++++---------- bamtk.c | 2 +- cleanup.sh | 12 ++ configure.ac | 108 ++++++++++++++++ misc/{Makefile => Makefile.generic} | 0 11 files changed, 579 insertions(+), 70 deletions(-) create mode 100644 Makefile.am rename Makefile => Makefile.generic (94%) create mode 100644 autogen.sh create mode 100644 cleanup.sh create mode 100644 configure.ac rename misc/{Makefile => Makefile.generic} (100%) 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.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 $@ maq2sam.c diff --git a/Makefile b/Makefile.generic similarity index 94% rename from Makefile rename to Makefile.generic index 25897db..002c71a 100644 --- a/Makefile +++ b/Makefile.generic @@ -21,7 +21,7 @@ all-recur lib-recur clean-recur cleanlocal-recur install-recur: wdir=`pwd`; \ list='$(SUBDIRS)'; for subdir in $$list; do \ cd $$subdir; \ - $(MAKE) CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ + $(MAKE) -f Makefile.generic CC="$(CC)" CXX="$(CXX)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ INCLUDES="$(INCLUDES)" LIBS="$(LIBS)" $$target || exit 1; \ cd $$wdir; \ done; 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.generic similarity index 100% rename from misc/Makefile rename to misc/Makefile.generic -- 2.39.2