0.5.10 mt fixes #1
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added 4 commits
January 2, 2013 17:09
Added the following wrappers that check the results of system calls and exit non-zero if something went wrong. This is so bwa can be more robust against system failures (e.g. IO errors from remote storage, or running out of memory). The existing and new wrappers have also been modified so that they no longer try to dump core on failure. In most cases the resulting core files are not useful (especially if bwa was compiled with optimization turned on) so just pollute whatever directories they got written to. The err_fflush wrapper also now calls fsync on regular files to try to ensure that data has been written out when using remote filesystems. This is not really necessary for local filesystems but only takes a few seconds to do. The fsync can be disabled by removing the #define for FSYNC_ON_FLUSH in utils.c. Wrappers for memory allocation functions: xcalloc xmalloc xrealloc xstrdup New wrappers for IO functions: err_fwrite err_fread_noeof (also dies on EOF) err_gzread err_fseek err_rewind err_ftell err_fprintf err_printf err_fflush err_fclose err_gzclose
Use the wrapper functions in utils.c plus a few extra bits of error checking code to catch system errors and exit non-zero when they occur. This commit mainly covers funtions that make IO system calls. Updated dependencies in Makefiles.
Use the wrapper functions in utils.c to catch system errors and exit non-zero when they occur. This commit adds wrappers for memory allocation functions (malloc, calloc, realloc and strdup). It also prevents gen_cigar from trying to realloc a buffer to zero bytes long. Updates the dependencies in the Makefile again.
Added wrappers err_fputc and err_fputs to catch failures in fput and fputs. Macros err_putchar and err_puts call the new wrappers and can be used in place of putchar and puts. To avoid having to make millions of function calls when printing out sequences, the code to print them in bwa_print_sam1 using putchar has been replaced by a new version in bwa_print_seq that puts the sequence into a buffer and then outputs the lot with err_fwrite. In testing, the new code was slightly faster than the old version, with the added benefit that it will stop promptly if IO problems are detected.
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Merge in 0.5.10 multithreaded fixes from Rob Davies