fastq-tools
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dcjones
Small utilities for working with fastq sequence files.
I added an option so sort by sequence size. It seems to work. This might be useful.
Hello :) It appears that the -S flag doesn't do anything (fastq-sort just hags using 0% cpu), but using --seq works fine. I am running Debian Jessie, and I downloaded...
I'm running fastq-sample from the current HEAD like this: `./src/fastq-sample -n 10000 -o downsampled -s 12345
fastq-sample segfaults while subsampling a couple of fastq files: fastq-sample -n 900000 -o subsample first.fastq second.fastq ... open("subsample.2.fastq", O_WRONLY|O_CREAT|O_EXCL, 0600) = 6 fcntl(6, F_GETFL) = 0x8001 (flags O_WRONLY|O_LARGEFILE) fstat(6, {st_mode=S_IFREG|0600,...
I get this message while executing `./autogen.sh`. ``` user@ubuntu14-server $ ./autogen.sh Can't exec "libtoolize": No such file or directory at /usr/bin/autoreconf line 196. Use of uninitialized value in pattern match...
I added option --rlo to sort co-lexicographically (i.e., in reverse lexicographical order) by sequences. This might be useful for data structures based on the Burrows-Wheeler Tranform.
I was trying to use `fastq-sample` but I keep on getting the error: ``` Input files have differing numbers of entries (1882 != 1677) ``` ``` fastq-sample -n 100 -o...
I downloaded the tar.gz file and ran autogen.sh but got this error: configure.ac:35: error: possibly undefined macro: AC_PROG_LIBTOOL If this token and others are legitimate, please use m4_pattern_allow. See the...
Hello, when compiling I get the following warning: ``` fastq-qscale.c: In function ‘fastq_qualscale’: fastq-qscale.c:61:21: warning: ‘compat_scales’ may be used uninitialized in this function [-Wmaybe-uninitialized] return x && !(x & (x...
seeing some implicit function declarations issue while regression building 0.8.3 release ``` fastq-sample.c:162:9: error: call to undeclared library function 'snprintf' with type 'int (char *, unsigned long, const char *,...
