Skip to content
Browse files

add mention of halWiggle liftover in doc. increase version to 2.1

  • Loading branch information...
1 parent f4231fb commit 59b44f02323509c39fd71db92d3717c72f531f92 @glennhickey committed Dec 5, 2013
Showing with 6 additions and 2 deletions.
  1. +5 −1 README.md
  2. +1 −1 api/inc/halDefs.h
View
6 README.md
@@ -275,14 +275,18 @@ Annotations in [BED](http://genome.ucsc.edu/FAQ/FAQformat.html#format1), ie tab-
SequenceName StartPosition LastPosition+1
-can be lifted over between genomes using `halLiftover`. halLiftover does a base-by-base mapping between any two sequences in the alignment (following paralogy relations as well).
+can be lifted over between genomes using `halLiftover`. halLiftover does a base-by-base mapping between any two sequences in the alignment (following paralogy relations as well). The output is written in BED (default) or PSL format.
halLiftover mammals.hal human human_annotation.bed dog dog_annotation.bed
will map all annotations in human_annotation.bed, which must refer to sequences in the human genome, to their corresponding locations in dog (if they exist), outputting the resulting annotations in dog_annotation.bed
halLiftover attempts to autodetect the BED version of the input. This can be overried with the `--inVedVersion` option. Columns that are not described in the official BED specs can be optionally mapped as-is using the `--keepExtra` option.
+By default, halLiftover uses spaces and/or tabs to separate columns. To use only tabs (ie to allow spaces within names), use the `--tab` option.
+
+Annotations in [Wiggle](http://genome.ucsc.edu/goldenPath/help/wiggle.html) format can likewise be mapped using `halWiggleLiftover`
+
#### Alignability
The number of distinct genomes different bases of a set of target genomes align to can be computed using the `halAlignability` tool. The output is in `.wig` format.
View
2 api/inc/halDefs.h
@@ -22,7 +22,7 @@
/** Version of the library. Increase before the decimal means
* backward compatibility with files generated by previous versions
* is lost (see checking function in halCommon.h) */
-#define HAL_VERSION 2.0
+#define HAL_VERSION 2.1
/**
* An index in a genome (must be large enough to represent the

0 comments on commit 59b44f0

Please sign in to comment.
Something went wrong with that request. Please try again.