Issue with when using single thread

[sybrohee]

When working with only one thread (i.e. --threads = 1), the results are different from the results obtained with more than one thread.
Indeed, the "original variants" are altered (GROUP_ID is filled in, IN_GROUP stays empty) and the sample fields are all set to 0 while the "merged variants" are added (with relevant IN_GROUP).
When working in multithreaded mode, I have the expected results : no alteration of the original variant (IN_GROUP is filled in, GROUP_ID stays empty) and addition of the "merged variants" (with relevant IN_GROUP).

#### SINGLE THREAD (???)

chrX	19754920	rs7883332	C	G	11731.8	PASS	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0	GT:DP:AD:AF:GQ	./.:.:.:.:.
chrX	19754926	rs773922290	G	T	11683.8	PASS	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0	GT:DP:AD:AF:GQ	0/1:1163:827,336:0.288908:99

chrX	19754920	rs7883332	cgaactg	GgaactT	11707.8	.	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0	GT:DP:AD:AF:GQ	./.:.:.:.:.



##### MUTLTI THREAD (EXPECTED BEHAVIOUR)


chrX	19754920	rs7883332	C	G	11731.8	PASS	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0	GT:DP:AD:AF:GQ	0/1:1157:816,341:0.294728:99
chrX	19754926	rs773922290	G	T	11683.8	PASS	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0	GT:DP:AD:AF:GQ	0/1:1163:827,336:0.288908:99

chrX	19754920	rs7883332	cgaactg	GgaactT	11707.8	.	Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=chrX_19754920_0;IN_GROUP=;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0	GT:DP:AD:AF:GQ	./.:.:.:.:.