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

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commit 59b44f02323509c39fd71db92d3717c72f531f92 1 parent f4231fb
@glennhickey authored
Showing with 6 additions and 2 deletions.
  1. +5 −1 README.md
  2. +1 −1  api/inc/halDefs.h
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6 README.md
@@ -275,7 +275,7 @@ 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
@@ -283,6 +283,10 @@ will map all annotations in human_annotation.bed, which must refer to sequences
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.
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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
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