Entering edit mode
9.4 years ago
Alex Reynolds
35k
- Compilation improvements
- Shane Neph put in a great deal of work to enable parallel builds (e.g.,
make -j N
to build various targets in parallel). Depending on the end user's environment, this can speed up compilation time by a factor of 2, 4 or more. - Fixed numerous compilation warnings of debug builds of starch toolkit under RHEL6/GCC and OS X 10.10.1/LLVM.
- Shane Neph put in a great deal of work to enable parallel builds (e.g.,
New
bedops
features- Added
--chop
and--stagger
options to "melt" inputs into contiguous or staggered disjoint regions of equivalent size. - For less confusion, arguments for
--element-of
,--chop
and otherbedops
operations that take numerical modifiers no longer require a leading hyphen character. For instance,--element-of 1
is now equivalent to the former usage of--element-of -1
.
- Added
New
bedmap
features- The
--sweep-all
option reads through the entire map file without early termination and can help deal withSIGPIPE
errors. It adds to execution time, but the penalty is not as severe as with the use of--ec
. Using--ec
alone will enable error checking, but will now no longer read through the entire map file. The--ec
option can be used in conjunction with--sweep-all
, with the associated time penalties. (Another method for dealing with this issue is to override howSIGPIPE
errors are caught by the interpreter (bash
, Python, etc.) and retrapping them or ignoring them. However, it may not a good idea to do this as other situations may arise in production pipelines where it is ideal to trap and handle all I/O errors in a default manner.) - New
--echo-ref-size
and--echo-ref-name
operations report genomic length of reference element, and rename the reference element inchrom:start-end
format (useful for labeling rows for input formatrix2png
orR
or other applications).
- The
bedextract
- Fixed upper-bound bug that would cause incorrect output in some cases
Conversion scripts
- Brand new C99 binary called
convert2bed
, which wrapper scripts (bam2bed
, etc.) now call. No more Python version dependencies, and the C-based rewrite offers massive performance improvements over old Python-based scripts. - Added parallel
bam2starch
script, which parallelizes creation of Starch archive from very large BAM files in SGE environments. - Added bug fix for missing code in
starchcluster.gnu_parallel
script, where the final collation step was missing. - The
vcf2bed
script now accepts the--do-not-split
option, which prints one BED element for all alternate alleles.
- Brand new C99 binary called
Starch archival format and compression/extraction tools
- Added duplicate- and nested-element flags in v2.1 of Starch metadata, which denote if a chromosome contains one or more duplicate and/or nested elements. BED files compressed with
starch
v2.5 or greater, or Starch archives updated withstarchcat
v2.5 or greater will include these values in the archive metadata. - The
unstarch
extraction tool offers--has-duplicate
and--has-nested
options to retrieve these flag values for a specified chromosome (or for all chromosomes). - Added
--is-starch
option tounstarch
to test if specified input file is a Starch v1 or v2 archive. - Added bug fix for compressing BED files with
starch
, where the archive would not include the last element of the BED input, if the BED input lacked a trailing newline. The compression tools now include a routine for capturing the last line, if there is no newline.
- Added duplicate- and nested-element flags in v2.1 of Starch metadata, which denote if a chromosome contains one or more duplicate and/or nested elements. BED files compressed with
Documentation improvements
- Remade some image assets throughout the documents to support Retina-grade displays
- Updated Homebrew (homebrew-science) package installation instructions
I am using the command like this
It gives this error
BEDOPS binaries and scripts must be in your
PATH
. Either you'd modify thePATH
variable setting or just copy BEDOPS binaries and scripts to/usr/local/bin
(or similar).Thanks I did it yesterday and it worked