bugfix: ReviewConsensusVariants should not require grouped raw reads to

[nh13]

overlap each variant.

In some cases, the consensus call may change the span of the alignment
to cover a base that's not covered by any grouped raw read used in that
consensus.

Fixed #604

[nh13]

I used the test case found in #604 .

The below shows the error with some more debug information, where it's reviewing a variant position of 1101 , where there's are no raw grouped R2 reads covering that position, where the code expects some, since it did fined consensus R2 reads covering that position. This is due to differences in alignment between grouped and consensus reads. The fix is to just return a zero count for the raw grouped reads.

# grouped BAM
$samtools view -f 128 NEB5.ds.group.csort.bam | grep 54796
MN01352:2:000H33NT7:1:12108:17698:4526	147	pUC57_CTNNB1_WT	1102	60	29S117M	=	1097	-122	CCCTACACGACGCTCTTCAGATCTCAACTGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGTGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATTAGTGGGA	FFF6/FFFFFFFFAFFF//=FF/FA6AF/FFAFFFFFA/FFFFFFFFFFF//FAFFFFFFFFFFFFAF/FFFFFFFFFF6FFFA/FFFFF/FFF///FFFAFAAFFFAAFFFA/F=AFFFFF6FA/F/FAFF/FFFFF//FFFFFF	MC:Z:123M23S	MD:Z:55A53G7	MI:Z:54796	NM:i:2	MQ:i:60	AS:i:107	XS:i:0	RX:Z:TTGTCGAACCAGCGGAC

# consensus BAM
$ samtools view -f 128 NEB5.ds.cons.filtered.csort.bam | grep 54796
:54796	99	pUC57_CTNNB1_WT	1097	60	122M	=	1097	122	CANCAGTCTTACNTGGACNCTGGAATCCATTCNNGTGCCACTACCACAGCTNCNTCTCNGANTGGTAAANGCAATCCTGNGGAANNGGNTGNGGATNCCTCNCAAGTCCTGTATGAGTGGGA	@@#CCCCCC@CC#@CCCC#CCCCCC@CC@@CC##CCCC@CCCCCCCCCCCC#C#CCCC#C@#CCC@CCC#CCCC@CCC@#CCCC##CC#CC#C@@@#C@CC#CCCCCCC@CCCCCCCCCC@C	MC:Z:122M	MD:Z:2a9c5t13t0g17c1t4t2g7g9a4g0a2a2t4a4c20	cD:i:1	cE:f:0	PG:Z:bwa	RG:Z:A	MI:Z:54796	NM:i:17	cM:i:1	MQ:i:60	UQ:i:34	AS:i:122	RX:Z:TTGTCGAACCAGCGGAC	cd:B:s,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	ce:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
:54796	147	pUC57_CTNNB1_WT	1097	60	122M	=	1097	-122	CNACNGTCTTACCTNGACTCTGGAATNNATTCTGGTGCCACTACNACAGCTCCTTNTCTGNGTGGTNAAGNNNATCCTGAGGAAGAGGANGNGGATACNTCNCNAGTCNTGTATNNGTGGGA	@#@C#CC@CCCCC@#CCCCCCCCCCC##C@CCCCCCCCCCCC@C#CCCCCCCCCC#CCC@#CCCCC#CCC###CCC@C@@CCC@@CCC@#C#@CCCCC#C@#C#C@CC#CCCCC##CCCCCC	MC:Z:122M	MD:Z:1a2a9g11c0c16c10c4a5a3g0c0a16t1t6c2c1a4c5g0a6	cD:i:1	cE:f:0	PG:Z:bwa	RG:Z:A	MI:Z:54796	NM:i:20	cM:i:1	MQ:i:60	UQ:i:40	AS:i:107	RX:Z:TTGTCGAACCAGCGGAC	cd:B:s,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1	ce:B:s,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

$ java -Xmx8g -jar ~/work/git/fgbio/target/scala-2.13/fgbio-2.0.3-7326a777-SNAPSHOT.jar ReviewConsensusVariants -i CTNNB1_WT_interval_list -c NEB5.ds.cons.filtered.csort.bam -g NEB5.ds.group.csort.bam -r CTNNB1_WT.fa -o out
...
Exception in thread "main" java.lang.IllegalStateException: Could not find reads with MI 54796 for R2 at locus Variant(pUC57_CTNNB1_WT,1101,A,None,None)

[codecov-commenter]

Codecov Report

Merging #860 (a3340b0) into main (7326a77) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main     #860   +/-   ##
=======================================
  Coverage   95.64%   95.64%           
=======================================
  Files         125      125           
  Lines        7238     7238           
  Branches      480      479    -1     
=======================================
  Hits         6923     6923           
  Misses        315      315           

Flag	Coverage Δ
unittests	95.64% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
.../fulcrumgenomics/umi/ReviewConsensusVariants.scala	97.58% <100.00%> (ø)

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