From 9245b3f68e335fd92ba2f597bf6aa9fe77e45adc Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@gmail.com>
Date: Tue, 27 Jun 2023 20:20:59 +0000
Subject: [PATCH] Fixed '--only' issue

---
 .vscode/settings.json                |  1 +
 out/test_files_shortened_haploid.vcf | 17 +++++++++++++++++
 src/modvcfsamples/cli.py             |  2 +-
 3 files changed, 19 insertions(+), 1 deletion(-)
 create mode 100644 out/test_files_shortened_haploid.vcf

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 89c672d..1fdd1db 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -12,6 +12,7 @@
     "cSpell.words": [
         "bioconda",
         "CHROM",
+        "modvcfsamples",
         "pytest",
         "pyvcf",
         "vcfpy",
diff --git a/out/test_files_shortened_haploid.vcf b/out/test_files_shortened_haploid.vcf
new file mode 100644
index 0000000..4ea6019
--- /dev/null
+++ b/out/test_files_shortened_haploid.vcf
@@ -0,0 +1,17 @@
+##fileformat=VCFv4.1
+##fileDate=10122015_22h01m13s
+##source=SHAPEIT2.v837
+##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Gambian	Chinese	French	Brazilian	Nigerian	Pakistani	English	Colombian	Indian	Japanese
+1	846808	rs4475691	C	T	100	.	AC=1276;AN=5008;DP=20368	GT:GQ:DP	1|1|1|1:70:60	0|0|0|0:30:10	0|0|0|0:20:40	./.:0:0	0|0|0|0:70:60	0|0|0|0:90:30	0|0|0|0:80:70	0|0|0|0:50:80	./.:0:0	0|0|0|0:100:80
+1	846854	rs111957712	G	A	100	.	AC=114;AN=5008;DP=20538	GT:GQ:DP	./.:0:0	0|0|0|0:40:30	0|0|0|0:80:30	0|0|0|0:0:20	0|0|0|0:40:80	0|0|0|0:10:30	./.:0:0	./.:0:0	0|0|0|0:70:0	0|0|0|0:90:30
+1	846864	rs950122	G	C	100	.	AC=1116;AN=5008;DP=20582	GT:GQ:DP	1|1|1|1:60:0	0|0|0|0:20:0	0|0|0|0:90:70	0|0|0|0:80:50	0|0|0|0:80:30	0|0|0|0:10:80	0|0|0|0:100:20	0|0|0|0:30:40	./.:0:0	0|0|0|0:30:90
+1	847228	rs3905286	C	T	100	.	AC=1215;AN=5008;DP=20731	GT:GQ:DP	1|1|1|1:70:80	0|0|0|0:90:80	0|0|0|0:60:50	0|0|0|0:60:90	0|0|0|0:30:40	0|0|0|0:70:10	0|0|0|0:100:80	0|0|0|0:100:50	0|0|0|0:70:100	0|0|0|0:40:40
+1	847297	rs11507768	G	A	100	.	AC=359;AN=5008;DP=20809	GT:GQ:DP	1|1|1|1:0:60	0|0|0|0:10:30	0|0|0|0:80:60	./.:0:0	0|0|0|0:10:100	0|0|0|0:10:100	./.:0:0	0|0|0|0:100:40	0|0|0|0:20:20	0|0|0|0:10:0
+1	847491	rs28407778	G	A	100	.	AC=1262;AN=5008;DP=16939	GT:GQ:DP	1|1|1|1:0:100	0|0|0|0:70:40	0|0|0|0:0:60	0|0|0|0:90:90	0|0|0|0:90:90	./.:0:0	0|0|0|0:70:60	0|0|0|0:70:0	0|0|0|0:90:100	0|0|0|0:60:60
+1	848023	rs144407116	C	A	100	.	AC=52;AN=5008;DP=22562	GT:GQ:DP	0|0|0|0:10:60	0|0|0|0:20:80	0|0|0|0:20:50	0|0|0|0:20:90	0|0|0|0:90:10	0|0|0|0:70:60	0|0|0|0:40:30	0|0|0|0:60:0	0|0|0|0:40:40	0|0|0|0:10:10
+1	848090	rs4246505	G	A	100	.	AC=857;AN=5008;DP=19301	GT:GQ:DP	0|0|0|0:70:70	0|0|0|0:90:30	0|0|0|0:40:10	0|0|0|0:80:20	0|0|0|0:50:50	0|0|0|0:10:30	./.:0:0	0|0|0|0:20:60	./.:0:0	0|0|0|0:90:0
+1	848445	rs4626817	G	A	100	.	AC=1255;AN=5008;DP=18444	GT:GQ:DP	1|1|1|1:100:40	0|0|0|0:80:90	0|0|0|0:30:100	0|0|0|0:100:60	0|0|0|0:40:90	0|0|0|0:20:30	0|0|0|0:70:100	./.:0:0	./.:0:0	0|0|0|0:80:30
+1	848456	rs11507767	A	G	100	.	AC=1266;AN=5008;DP=18137	GT:GQ:DP	1|1|1|1:40:30	./.:0:0	0|0|0|0:60:90	0|0|0|0:60:40	0|0|0|0:100:80	0|0|0|0:50:50	0|0|0|0:0:10	0|0|0|0:60:0	0|0|0|0:100:100	./.:0:0
+1	848738	rs3829741	C	T	100	.	AC=855;AN=5008;DP=16663	GT:GQ:DP	0|0|0|0:50:90	0|0|0|0:50:50	0|0|0|0:50:30	0|0|0|0:60:60	0|0|0|0:80:40	0|0|0|0:50:80	0|0|0|0:0:80	0|0|0|0:0:30	0|0|0|0:10:0	0|0|0|0:70:30
diff --git a/src/modvcfsamples/cli.py b/src/modvcfsamples/cli.py
index 6eeacc2..505e827 100644
--- a/src/modvcfsamples/cli.py
+++ b/src/modvcfsamples/cli.py
@@ -8,7 +8,7 @@ def run(vcfs: list[str], only: list[str], gt: Union[int, None], output_dir: str)
         vcf_records, header = sample.get_records_from_vcf(vcf)
         modified_vcfs = vcf_records
         modified_header = header
-        if len(only) > 1:
+        if len(only) > 0:
             modified_vcfs, modified_header = sample.keep_specific_call_data(modified_vcfs, modified_header, *only)
         if gt is not None:
             modified_vcfs, modified_header = sample.normalize_gt_to_length(modified_vcfs, modified_header, gt)