Closed timbitz closed 6 years ago
Merging #69 into master will increase coverage by
4.52%
. The diff coverage is75.36%
.
@@ Coverage Diff @@
## master #69 +/- ##
==========================================
+ Coverage 54.27% 58.79% +4.52%
==========================================
Files 18 19 +1
Lines 2320 2378 +58
==========================================
+ Hits 1259 1398 +139
+ Misses 1061 980 -81
Impacted Files | Coverage Δ | |
---|---|---|
src/edges.jl | 72.58% <ø> (ø) |
:arrow_up: |
src/index.jl | 10.29% <0%> (-0.64%) |
:arrow_down: |
src/quant.jl | 59.32% <0%> (+2.62%) |
:arrow_up: |
src/graph.jl | 93.69% <100%> (+0.18%) |
:arrow_up: |
src/types.jl | 91.67% <100%> (+4.17%) |
:arrow_up: |
src/align.jl | 71.63% <28.57%> (-0.5%) |
:arrow_down: |
src/io.jl | 59.24% <72.5%> (+26.18%) |
:arrow_up: |
src/bam.jl | 92.31% <92.31%> (ø) |
|
src/refset.jl | 92% <94.74%> (-1.37%) |
:arrow_down: |
... and 3 more |
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact)
,ø = not affected
,? = missing data
Powered by Codecov. Last update bed4f75...a7744b4. Read the comment docs.
This is a fairly major pull request with changes primarily affecting Whippet's indexing capabilities. This branch enables a user to supplement standard-annotation files with more sources of splice-sites for Whippet to utilize when indexing/building CSG nodes. These changes allow Whippet to produce more comprehensive CSGs in poorly annotated species, utilizing unannotated splice-sites (and therefore also unannotated exons) from read alignments in a pre-existing BAM file created by another program with novel spliced-read alignment abilities.
Specific changes are:
--bam
parameter (whippet-index.jl
)refset.jl
)--bam-both-novel
flag.graph.jl
)--bam
parameter.--refflat
flag (whippet-index.jl
)..exons.gz
file fromwhippet-index.jl
that maps all putative exons in the Whippet index to the corresponding Whippet nodes and their annotation status.Prior to merging, testing the PR should be possible with:
Sorted and Indexed BAM files can be created with
samtools
as followsThen build an index but with the additional
--bam filename.sort.rmdup.bam
parameter, which also looks forfilename.sort.rmdup.bam.bai