ea-utils
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ExpressionAnalysis
sam-stats doesn't support -o and -O option
What steps will reproduce the problem?
$ /software/ea-utils/ea-utils-svn/clipper/sam-stats -O test.sam-stats test.bam
/software/ea-utils/ea-utils-svn/clipper/sam-stats: invalid option -- 'O'
Unknown option `-O'.
Usage: sam-stats [options] [file1] [file2...filen]
Version: 1.37.657
...
What is the expected output? What do you see instead?
What version of the product are you using? On what operating system?
svn version of ea-utils
Here is a patch (options also sorted alphabetically):
$ svn diff
Index: sam-stats.cpp
===================================================================
--- sam-stats.cpp (revision 662)
+++ sam-stats.cpp (working copy)
@@ -222,7 +222,7 @@
int long_index=0;
const char *prefix;
- while ( (c = getopt_long(argc, argv, "?BArR:Ddx:MhS:", long_options,
&long_index)) != -1) {
+ while ( (c = getopt_long(argc, argv, "?ABDdhMoO:R:rS:x:", long_options,
&long_index)) != -1) {
switch (c) {
case 'd': ++debug; break; // increment debug level
case 'D': ++trackdup; break;
After this patch, this option is accepted, but it doesn't do anything as far as
I can tell because the prefix variable is never used afterwards:
$ grep prefix sam-stats.cpp
const char *prefix;
case 'O': prefix=optarg; break;
"-O PREFIX Output prefix enabling extended output (see below)\n"
Here is some bash code to extract the info:
$ echo " case 'd': ++debug; break;
// increment debug level
case 'D': ++trackdup; break;
case 'B': inbam=1; break;
case 'A': max_chr=1000000; break; // max chrom
case 'R': rnafile=optarg; // pass through
case 'r': max_chr=1000000; rnamode=1; if (histnum < 60) histnum=60; break;
case 'O': prefix=optarg; break;
case 'S': histnum=atoi(optarg); break;
case 'x': ext=optarg; break;
case 'M': newonly=1; break;
case 'o': fq_out=1; trackdup=1; break; // output suff
case 'h': usage(stdout); return 0;
case '?':
"| grep -E -o "'.?'" |cut -f2 -d "'" | cut -f2 -d "'"| sort | tr -d '\n'
?ABdDhMoOrRSx
Similar problems exist in other tools ( I didn't check all of them ):
For example: fastq-join.c:
There is a check for "-dRnbeo:t:v:m:p:r:", but options "-nbe" don't exist.
Also in the help "-t" is not mentioned (as is "-d" which is OK as it is a debug
option).
while ( (c = getopt (argc, argv, "-dRnbeo:t:v:m:p:r:")) != -1) {
switch (c) {
case '\1':
if (!in[0])
in[0]=optarg;
else if (!in[1])
in[1]=optarg;
else if (!in[2])
in[2]=optarg;
else {
usage(stderr); return 1;
}
++in_n;
break;
case 'o': if (out_n == 3) {
usage(stderr); return 1;
}
out[out_n++] = optarg;
break;
case 'r': orep = optarg; break;
case 't': threads = atoi(optarg); break;
case 'm': mino = atoi(optarg); break;
case 'p': pctdiff = atoi(optarg); break;
case 'R': norevcomp = true; break;
case 'd': debug = 1; break;
case 'v':
if (strlen(optarg)>1) {
fprintf(stderr, "Option -v requires a single character argument");
exit(1);
}
verify = *optarg; break;
case '?':
if (strchr("otvmpr", optopt))
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (isprint(optopt))
fprintf (stderr, "Unknown option `-%c'.\n", optopt);
else
fprintf (stderr,
"Unknown option character `\\x%x'.\n",
optopt);
usage(stderr);
return 1;
}
}
Original issue reported on code.google.com by [email protected] on 9 Oct 2013 at 2:35
I'm not 100% certain the -O output even works. I think the usage lines might
have been written before the function. I'll be happy to add the patch if you
say... yes: I patched it and it outputs all the files correctly.
Original comment by [email protected] on 2 May 2014 at 5:00
We have get this up on github ... makes more sense.
Original comment by [email protected] on 2 May 2014 at 5:01
Hi, I wanted to try the extended output today and found out this bug is still not solved? I installed it via apt-get on ubuntu and still get the error :
/usr/bin/sam-stats: invalid option -- 'O' Unknown option `-O'.
Im running Version: 1.38.681 on Ubuntu 20.04.3 LTS
Will this be fixed in the future?
Best, Nadine
