I encountered an error when trying to open a BAM stream on stdin with bamToBed
from bedtools 2.12.0 on Solaris. I dumped part of the BAM stream to a file and
succeeded in opening the file using "bamToBed -i", but was unable to open the
same BAM file when read from stdin:
########################################
$ bamToBed -i test.bam | head -n 1
Gm19 38182344 38182807 F1RQIAA01A000V 255 +
$ bamToBed < test.bam
BGZF ERROR: unable to open file stdin
########################################
The partial BAM file could be read from stdin on OS X 10.5, however.
Some debugging revealed that the issue occurs in BGZF.cpp, lines 245-256:
########################################
// read BGZF data from stdin
else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) )
Stream = freopen(NULL, mode, stdin);
// write BGZF data to stdout
else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) )
Stream = freopen(NULL, mode, stdout);
if ( !Stream ) {
printf("BGZF ERROR: unable to open file %s\n", filename.c_str() );
return false;
}
########################################
The Solaris freopen() man page indicates that it behave in a nonstandard manner
(always returns NULL if the first argument is NULL) unless "the application
conforms to SUSv3" (i.e., the _XOPEN_SOURCE feature test macro is defined with
the value 600).
A simple solution is to bypass the call to freopen, which should be unnecessary
for stdin and stdout, and simply assign stdin/stdout to Stream (see the
attached patch).
--
Nathan Weeks
USDA-ARS
SoyBase http://soybase.org
Original issue reported on code.google.com by nate.we...@gmail.com on 11 Jul 2011 at 4:37
Original issue reported on code.google.com by
nate.we...@gmail.comon 11 Jul 2011 at 4:37Attachments: