csi stuff

bump version. document how to use CSI and adjust env vars to take
advantange

.travis.yml

@@ -5,10 +5,10 @@ os:
   - osx
 
 go:
-  - 1.6
   - 1.7
   - 1.8
-  - tip
+  - 1.9
+  - 1.10
 
 before_install:
   - go get github.com/axw/gocov/gocov

README.md

@@ -2,7 +2,8 @@ vcfanno
 =======
 <!--
 build:
- VERSION=0.1.0; goxc -build-ldflags "-X main.VERSION=$VERSION" -include docs/,example/,README.md -d /tmp/vcfanno/ -pv=$VERSION -bc='linux,darwin,windows,!arm'
+ CGO_ENABLED=0 GOARCH=amd64 go build -o vcfanno_linux64 --ldflags '-extldflags "-static"' vcfanno.go
+ GOOS=darwin GOARCH=amd64 CGO_ENABLED=0 go build -o vcfanno_osx --ldflags '-extldflags "-static"' vcfanno.go
 -->
 
 

docs/CHANGES.md

@@ -1,3 +1,7 @@
+v0.2.9
+------
++ support for CSI indexes. If present, a .csi file will be preferred over a .tbi.
+
 v0.2.8
 ------
 + fix fo #71 for out of bounds warning followed by panic.

docs/performance_tips.md

@@ -23,6 +23,23 @@ default value is 100. For example:
 GOGC=2000 vcfanno -p 12 a.conf a.vcf
 ```
 
+CSI
+---
+
+For very dense files such as CADD, or even gnomAD or ExAC, it is recommended to index
+with csi, this allows finer resolution in the index. When a .csi file is present, `vcfanno`
+will prefer it over a .tbi. For example, using:
+
+```
+tabix -m 12 --csi $file
+```
+
+will work for most cases. When a csi is present, it seems to be best to lower the
+`IRELATE_MAX_GAP` (see below) to 1000 or lower. Doing this, we can see a **50 % speed improvement** when
+using a csi-index ExAC file to annotate a clinvar file.
+
+Experiment with what works best for each scenario.
+
 Max Gap / Chunk Size
 --------------------
 
@@ -37,7 +54,8 @@ sets, it is best to have this value be large so that each annotation worker
 gets enough work to keep it busy.
 
 The default gap size is `5000` bases. Users can alter this using the
-environment variable `IRELATE_MAX_GAP`.
+environment variable `IRELATE_MAX_GAP`. When using a csi index this can
+be much lower, for example `1000`
 
 The default chunk size is `8000` query intervals. Users can alter this using the
 environment variable `IRELATE_MAX_CHUNK`.

tests/release-tests.sh

@@ -14,10 +14,11 @@ BASE=/data/gemini_install/data/gemini_data/
 go build -a
 V=./vcfanno
 
-IRELATE_MAX_GAP=500 run clinvar_common_pathogenic $V -lua docs/examples/clinvar_exac.lua -p 4 -base-path $BASE docs/examples/clinvar_exac.conf $BASE/clinvar_20170130.tidy.vcf.gz
+GOGC=900 IRELATE_MAX_GAP=600 run clinvar_common_pathogenic $V -lua docs/examples/clinvar_exac.lua -p 4 -base-path $BASE docs/examples/clinvar_exac.conf $BASE/clinvar_20170130.tidy.vcf.gz
 assert_equal 577 $(zgrep -wc common_pathogenic $STDOUT_FILE)
 assert_equal $(zgrep -cv ^# $STDOUT_FILE) $(zgrep -cv ^# $BASE/clinvar_20170130.tidy.vcf.gz)
 
+exit 0
 #tail -1 $STDERR_FILE
 
 run exac_combine vcfanno -base-path $BASE docs/examples/exac_combine/exac_combine.conf $BASE/ExAC.r0.3.sites.vep.tidy.vcf.gz 

vcfanno.go

@@ -25,7 +25,7 @@ import (
 	"github.com/brentp/xopen"
 )
 
-var VERSION = "0.2.8"
+var VERSION = "0.2.9"
 
 func envGet(name string, vdefault int) int {
 	sval := os.Getenv(name)