0.0.10 release stuff

example/custom.lua

@@ -110,7 +110,7 @@ join = table.concat
 
 function check_clinvar_aaf(clinvar_sig, max_aaf_all, aaf_cutoff)
     -- didn't find an aaf for this so can't be common
-    if max_aaf_all == nil then
+    if max_aaf_all == nil or clinvar_sig == nil then
         return false
     end
     if type(clinvar_sig) ~= "string" then

example/gem.conf

@@ -5,11 +5,23 @@ names = ["in_exac_flag", "ac_exac_all", "an_exac_all", "ac_exac_afr", "an_exac_a
 
 ops=["flag", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self"]
 
+[[annotation]]
+file="ESP6500SI.all.snps_indels.tidy.v2.vcf.gz"
+fields=["TAC", "EA_AC", "AA_AC", "TAC", "EXOME_CHIP"]
+names=["in_esp_flag", "aaf_esp_ea_float", "aaf_esp_aa_float", "aaf_esp_all_float", "EXOME_CHIP_flag"]
+ops=["flag", "lua:ratio(vals)", "lua:ratio(vals)", "lua:ratio(vals)", "flag"]
+
+[[annotation]]
+file="dbsnp.b141.20140813.hg19.tidy.vcf.gz"
+fields=["ID"]
+names=["rs_ids"]
+ops=["concat"]
+
 [[annotation]]
 file="ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz"
 fields=["AF", "AMR_AF", "EAS_AF", "SAS_AF", "AFR_AF", "EUR_AF", "AF"]
 names=["in_1kg_flag", "aaf_1kg_amr_float", "aaf_1kg_eas_float", "aaf_1kg_sas_float", "aaf_1kg_afr_float", "aaf_1kg_eur_float", "aaf_1kg_all_float"]
-ops=["flag", "max", "max", "max", "max", "max", "max"]
+ops=["flag", "self", "self", "self", "self", "self", "self"]
 
 [[annotation]]
 file="clinvar_20150305.tidy.vcf.gz"
@@ -33,13 +45,8 @@ type="Flag"
 file="cosmic-v68-GRCh37.tidy.vcf.gz"
 fields=["ID"]
 names=["cosmic_ids"]
-ops=["concat"]
+ops=["uniq"]
 
-[[annotation]]
-file="dbsnp.b141.20140813.hg19.tidy.vcf.gz"
-fields=["ID"]
-names=["rs_ids"]
-ops=["concat"]
 
 [[annotation]]
 file="hg19_fitcons_fc-i6-0_V1-01.bed.gz"
@@ -48,11 +55,6 @@ names=["fitcons_float"]
 ops=["mean"]
 
 
-[[annotation]]
-file="ESP6500SI.all.snps_indels.tidy.v2.vcf.gz"
-fields=["TAC", "EA_AC", "AA_AC", "TAC", "EXOME_CHIP"]
-names=["in_esp_flag", "aaf_esp_ea_float", "aaf_esp_aa_float", "aaf_esp_all_float", "EXOME_CHIP_flag"]
-ops=["flag", "lua:ratio(vals)", "lua:ratio(vals)", "lua:ratio(vals)", "flag"]
 
 #[[annotation]]
 #file="LCR-hs37d5.bed.gz"
@@ -83,13 +85,13 @@ names=[ "encode_consensus_gm12878", "encode_consensus_h1hesc", "encode_consensus
 file="hg19.gwas.bed.gz"
 columns=[4]
 names=["gwas_pubmed_trait"]
-ops=["concat"]
+ops=["uniq"]
 
 [[annotation]]
 file="hg19.rmsk.bed.gz"
 columns=[4]
 names=["rmsk"]
-ops=["concat"]
+ops=["uniq"]
 
 [[annotation]]
 file="hg19.gerp.elements.bed.gz"
@@ -107,13 +109,13 @@ ops=["flag"]
 file="hg19.dgv.bed.gz"
 columns=[4]
 names=["dgv"]
-ops=["concat"]
+ops=["uniq"]
 
 [[annotation]]
 file="wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz"
 columns=[4]
 names=["tfbs"]
-ops=["concat"]
+ops=["uniq"]
 
 [[annotation]]
 file="genetic_map_HapMapII_GRCh37.gz"
@@ -125,7 +127,7 @@ names=["hapmap1", "hapmap2"]
 [[annotation]]
 file="stam.125cells.dnaseI.hg19.bed.gz"
 columns=[5, 6]
-ops=["mean", "concat"]
+ops=["mean", "uniq"]
 names=["stam_mean", "stam_names"]
 
 [[annotation]]

tests/release-tests.sh

@@ -12,14 +12,19 @@ BASE=/usr/local/src/gemini_install//data/gemini_data/
 
 V=vcfanno
 
-IRELATE_VERBOSE=TRUE IRELATE_MAX_CHUNK=1 run clinvar_common_pathogenic $V -lua docs/examples/clinvar_exac.lua -p 4 -base-path $BASE docs/examples/clinvar_exac.conf $BASE/clinvar_20150305.tidy.vcf.gz
+IRELATE_VERBOSE=TRUE 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_20150305.tidy.vcf.gz
 assert_equal 567 $(zgrep -wc common_pathogenic $STDOUT_FILE)
 assert_equal $(zgrep -cv ^# $STDOUT_FILE) $(zgrep -cv ^# $BASE/clinvar_20150305.tidy.vcf.gz)
 
 tail -1 $STDERR_FILE
 
-#run exac_combine vcfanno -base-path $BASE $BASE/ExAC.r0.3.sites.vep.tidy.vcf.gz docs/examples/exac_combine/exac_combine.conf
+run exac_combine vcfanno -base-path $BASE $BASE/ExAC.r0.3.sites.vep.tidy.vcf.gz docs/examples/exac_combine/exac_combine.conf
 
-IRELATE_MAX_CHUNK=2 IRELATE_MAX_GAP=10 run filehandletest $V -lua example/custom.lua -p 4 -base-path $BASE example/gem.conf $BASE/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz | head -1000 | python tests/find-out-of-order.py
+orun() {
+$V -lua example/custom.lua -p 4 -base-path $BASE example/gem.conf $BASE/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz | head -1000 | python tests/find-out-of-order.py
+
+}
+
+IRELATE_MAX_CHUNK=2 IRELATE_MAX_GAP=10 run filehandletest orun
 assert_exit_code 0
 assert_equal $(grep -c "too many open files" $STDERR_FILE) "0"

vcfanno.go

@@ -25,7 +25,7 @@ import (
 	"github.com/brentp/xopen"
 )
 
-var VERSION = "0.0.10-rc2"
+var VERSION = "0.0.10"
 
 func envGet(name string, vdefault int) int {
 	sval := os.Getenv(name)
@@ -154,8 +154,8 @@ see: https://github.com/brentp/vcfanno
 			lastMsg.RLock()
 			em := e.Error()
 			if em != lastMsg.s[0] && em != lastMsg.s[1] && em != lastMsg.s[2] {
-				lastMsg.RUnlock()
 				log.Println(e, ">> this error may occur many times. reporting once here...")
+				lastMsg.RUnlock()
 				lastMsg.Lock()
 				lastMsg.s[lastMsg.i] = em
 				if lastMsg.i == len(lastMsg.s)-1 {
@@ -170,7 +170,7 @@ see: https://github.com/brentp/vcfanno
 		}
 	}
 
-	maxGap := envGet("IRELATE_MAX_GAP", 5000)
+	maxGap := envGet("IRELATE_MAX_GAP", 20000)
 	maxChunk := envGet("IRELATE_MAX_CHUNK", 8000)
 
 	stream := irelate.PIRelate(maxChunk, maxGap, qstream, *ends, fn, queryables...)