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 ./.:.:.:.:.
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).