Merge pull request #13 from PacificBiosciences/extra_tracks

doc update for v0.13.1

Author: holtjma

CHANGELOG.md

@@ -1,3 +1,12 @@
+# v0.13.1
+## Changes
+- Adds two haplotype-specific tracks for `methbat segment`:
+  - `{OUT_PREFIX}.hap1.bedgraph` - Contains the underlying methylation values for haplotype 1 for each segmented region
+  - `{OUT_PREFIX}.hap2.bedgraph` - Same as above, but for haplotype 2
+
+## Fixed
+- Fixed an issue where the BEDGRAPH outputs from `methbat segment` were reporting median values instead of the indicated mean values. This change did not alter the segmentation itself. However, since the value associated with each segment changed, the reported regions in `{OUT_PREFIX}.meth_regions.bed` may be altered to reflect the correct, mean values.
+
 # v0.13.0
 ## Changes
 - Beta release of a new signature mode, `methbat signature`, that will identify regions with different combined methylation in a case-control population. Greater details on usage can be found in the documentation for signature mode.

docs/segmentation_guide.md

@@ -30,3 +30,4 @@ Currently, all outputs follow standard BED or BEDGRAPH file formats, the content
 * `{OUT_PREFIX}.meth_regions.bed` - BED file with merged regions. The fourth column indicates the segment categorization: Methylated (M), Unmethylated (U), or AlleleSpecificMethylation (ASM).
 * `{OUT_PREFIX}.combined_methyl.bedgraph` - BEDGRAPH file with raw values from combined methylation segmentation. The fourth column indicates the combined methylation average for the segment; range 0.0 (unmethylated) to 1.0 (methylated).
 * `{OUT_PREFIX}.asm.bedgraph` - BEDGRAPH file with raw values from ASM segmentation. The fourth column indicates the ASM average for the segment, calculated as: (methylation of haplotype 2) - (methylation of haplotype 1); range -1.0 (H1 methylated, H2 unmethylated) to 1.0 (H1 unmethylated, H2 methylated).
+* `{OUT_PREFIX}.hap{1/2}.bedgraph` - BEDGRAPH file with the raw values from haplotype-specific segmentation. The fourth column indicates the methylation average for the segment for the specific haplotype; range 0.0 (unmethylated) to 1.0 (methylated).