From 8c692e2de47ec435cbe4f87744c671aa3d2f8015 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Thu, 18 Jul 2019 19:38:32 -0600
Subject: [PATCH] handle by_alt + float correctly

closes #113
---
 api/api.go                               |   7 +++++++
 tests/by_alt_float/annotation.tsv.gz     | Bin 0 -> 237 bytes
 tests/by_alt_float/annotation.tsv.gz.tbi | Bin 0 -> 99 bytes
 tests/by_alt_float/conf.toml             |   5 +++++
 tests/by_alt_float/q.vcf                 |   7 +++++++
 tests/functional-test.sh                 |   7 +++++++
 6 files changed, 26 insertions(+)
 create mode 100644 tests/by_alt_float/annotation.tsv.gz
 create mode 100644 tests/by_alt_float/annotation.tsv.gz.tbi
 create mode 100644 tests/by_alt_float/conf.toml
 create mode 100644 tests/by_alt_float/q.vcf

diff --git a/api/api.go b/api/api.go
index e8f9059..cf470f3 100644
--- a/api/api.go
+++ b/api/api.go
@@ -540,6 +540,13 @@ func (s *Source) UpdateHeader(r HeaderUpdater, ends bool, htype string, number s
 	if s.Op == "by_alt" {
 		number = "A"
 		ntype = "String"
+		if strings.HasSuffix(s.Name, "_float") {
+			ntype = "Float"
+			s.Name = s.Name[:len(s.Name)-6]
+		} else if strings.HasSuffix(s.Name, "_int") {
+			ntype = "Integer"
+			s.Name = s.Name[:len(s.Name)-4]
+		}
 		// for 'self' and 'first', we can get the type from the header of the annotation file.
 	} else if htype != "" && (s.Op == "self" || s.Op == "first") {
 		ntype = htype
diff --git a/tests/by_alt_float/annotation.tsv.gz b/tests/by_alt_float/annotation.tsv.gz
new file mode 100644
index 0000000000000000000000000000000000000000..6a4373a1393465286c04b50c0139ae904ed5ad9b
GIT binary patch
literal 237
zcmb2|=3rp}f&Xj_PR>jW7Z`lcY|J}kAkgse=O+>M)Xb&F4jsuooH41Z#CfGwn)c2k
z(|Y)Cs&#B{pZIisU2SUT+ILnqJZsm^&YJ4<@b-_s{|DEKOg>%yMABa^QheH(hs?iU
zPq7HO6~E@-{Rx{+U-z*nKC<_*&tl#;l{*)63cu5=5|7)aer@u{n~%zrU%#5^w&0uG
z;^-Vd3C+NmOd;2sw@##66g4%bU9dZxkXNtl-jr<rr{t*Els`fD7d&K;{<w2;Z^#9X
at*g7)8@Rt@TnG9?9?e7249sBvfd~NU<!Cnm

literal 0
HcmV?d00001

diff --git a/tests/by_alt_float/annotation.tsv.gz.tbi b/tests/by_alt_float/annotation.tsv.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..f4a615f554b8c02cbf1eb0773a851d8eb1dbcdfe
GIT binary patch
literal 99
zcmb2|=3rp}f&Xj_PR>jWZVcRopHfm%8W;r5vK&1XU?^~#!>7u(>BBdJ0|#7p=%qZ+
iWf61^Ki;F#=69HZL1eMm`97d-c{F3B8JIzaf&l=oG#Qlu

literal 0
HcmV?d00001

diff --git a/tests/by_alt_float/conf.toml b/tests/by_alt_float/conf.toml
new file mode 100644
index 0000000..d0468ac
--- /dev/null
+++ b/tests/by_alt_float/conf.toml
@@ -0,0 +1,5 @@
+[[annotation]]
+names = ["CADD_RAW_float"]
+file = "annotation.tsv.gz"
+columns = [5]
+ops = ["by_alt"]
diff --git a/tests/by_alt_float/q.vcf b/tests/by_alt_float/q.vcf
new file mode 100644
index 0000000..791d665
--- /dev/null
+++ b/tests/by_alt_float/q.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##contig=<ID=chr2,length=242193529,assembly=GRCh38>
+##INFO=<ID=AF,Number=.,Type=Float,Description="">
+##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
+##hailversion=0.2.9-8588a25687af
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr2	41647	2_41647_A_G	A	G	1328.0	.	AF=1.56250e-02;AQ=1328
diff --git a/tests/functional-test.sh b/tests/functional-test.sh
index ab6dd3c..11aa5b6 100755
--- a/tests/functional-test.sh
+++ b/tests/functional-test.sh
@@ -187,3 +187,10 @@ run self_test_with_A_and_many_overlaps fn_self_test_with_A_and_many_overlaps
 assert_exit_code 0
 assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AC=35,65;GN_AF=0.3717,0.6122"
 assert_in_stdout "ID=GN_AF,Number=A"
+
+
+run check_by_alts_float vcfanno -base-path tests/by_alt_float/ tests/by_alt_float/conf.toml tests/by_alt_float/q.vcf
+assert_exit_code 0
+assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AF=1.56250e-02;AQ=1328;CADD_RAW=0.591814"
+go install -a
+