* avoid a segfault when network connect fails

 * update INSTALL
 * fixed a bug in tview on big-endian by Nathan Weeks

diff --git a/INSTALL b/INSTALL
index f1cf7aa4079ca1302608dd81c59a7882597975ee..37d84a9e48b3247f8b807d7d983e182e17bb1204 100644 (file)
--- a/INSTALL
+++ b/INSTALL
@@ -1,29 +1,30 @@
 System Requirements
 ===================
 
-SAMtools depends on the zlib library <http://www.zlib.net>. The latest
-version 1.2.3 is preferred and with the latest version you can compile
-razip and use it to compress a FASTA file. SAMtools' faidx is able to
-index a razip-compressed FASTA file to save diskspace. Older zlib also
-works with SAMtools, but razip cannot be compiled.
+SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
+preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
+file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
+diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.
 
 The text-based viewer (tview) requires the GNU ncurses library
-<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and
-most of the modern Linux/Unix distributions. If you do not have this
-library installed, you can still compile the rest of SAMtools by
-manually modifying one line in Makefile.
+<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
+the modern Linux/Unix distributions. If you do not have this library installed,
+you can still compile the rest of SAMtools by manually changing:
+`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
+comment out the line starting with `LIBCURSES='.
 
 
 Compilation
 ===========
 
-Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can
-compile razip with `make razip'.
+Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
+razip with `make razip'.
 
 
 Installation
 ============
 
-Simply copy `samtools' and other executables/scripts in `misc' to a
-location you want (e.g. a directory in your $PATH). No further
-configurations are required.
+Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
+a location you want (e.g. a directory in your $PATH). You may also copy
+`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
+that the `man' command may find the manual.

diff --git a/bam_tview.c b/bam_tview.c
index e48afa7bd4add26404fecc04d6548e7b3989927b..bf01e15c3d79b1a55920bd4162c8e347b9f1f0d7 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -183,12 +183,12 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
 {
        tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
        tv->is_dot = 1;
-       tv->idx = bam_index_load(fn);
-       if (tv->idx == 0) exit(1);
        tv->fp = bam_open(fn, "r");
        bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
        assert(tv->fp);
        tv->header = bam_header_read(tv->fp);
+       tv->idx = bam_index_load(fn);
+       if (tv->idx == 0) exit(1);
        tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
        if (fn_fa) tv->fai = fai_load(fn_fa);
        tv->bmc = bam_maqcns_init();

diff --git a/knetfile.c b/knetfile.c
index 1e2c042701de0fec88212f563ff4862da6fcad93..af091465862c238aefeb3d0562b03f75320b6c1d 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -1,6 +1,7 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2008 by Genome Research Ltd (GRL).
+                 2010 by Attractive Chaos <attractor@live.co.uk>
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -23,11 +24,9 @@
    SOFTWARE.
 */
 
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
 /* Probably I will not do socket programming in the next few years and
    therefore I decide to heavily annotate this file, for Linux and
-   Windows as well.  -lh3 */
+   Windows as well.  -ac */
 
 #include <time.h>
 #include <stdio.h>
@@ -90,7 +89,7 @@ static int socket_connect(const char *host, const char *port)
 
        int on = 1, fd;
        struct linger lng = { 0, 0 };
-       struct addrinfo hints, *res;
+       struct addrinfo hints, *res = 0;
        memset(&hints, 0, sizeof(struct addrinfo));
        hints.ai_family = AF_UNSPEC;
        hints.ai_socktype = SOCK_STREAM;