!LAUNCH: crac -i ${abs_top_builddir:-../..}/test_f/causes/genome -r snp.fa -k 22 --deep-snv --nb-nucleotides-snv-comparison 3 -o ${abs_top_builddir:-../..}/test_f/causes/snp.sam --detailed-sam --use-x-in-cigar
!OUTPUT_FILE: ${abs_top_builddir:-../..}/test_f/causes/snp.sam
!OUTPUT_DIR: ${abs_top_builddir:-../..}/test_f/causes

$One substitution in the middle of the read (A -> g)
4:^snp1-[1-4].*chr1.*\\s+1\\s+.*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:A:G

$snp1 revcomp
3:^snp1-rc-[1-3].*chr1.*\\s+1\\s+.*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:A:G

$One substitution in the middle of the read, heterozygous (T -> a, T -> c)
4:^snp2-[1-4].*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:T:A
4:^snp2-[5-9].*\\s+(60M|28M1.31M)\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:T:C

$Two substitutions, close one to the other (A -> c, A -> c)
4:^snp3-[1-4].*\\s+(60M|27M1.2M1.29M)\\s+.*XE:Z:0:0:SNP:[^:]+:27:[^:]+:A:C;1:0:SNP:[^:]+:30:[^:]+:A:C

$One substitution close to the start of the read (G -> c). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
4:^snp4-[1-4].*chr1\\s+181\\s+.*\\s+(60M|3M1.56M)\\s+.*XE:Z:0:0:SNP:[^:]+:3:[^:]+:G:C

$Revcomp of snp4. 
3:^snp4-rc-[1-3].*chr1\\s+181\\s+.*\\s+(60M|3M1.56M)\\s+.*XE:Z:0:0:SNP:[^:]+:3:[^:]+:G:C

$One substitution close to the end of the read (G -> c) + bioundetermined before that (T > a in pos 0). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
3:^snp5-[1-3].*chr1\\s+242\\s+.*\\s+(60M|1.55M1.3M)\\s+.*;1:1:SNP:[^:]+:56:[^:]+:G:C

$Revcomp of snp5
3:^snp5-rc-[1-3].*chr1\\s+242\\s+.*\\s+(60M|1.55M1.3M)\\s+.*XE:Z:.*;0:1:SNP:[^:]+:56:[^:]+:G:C

$One deletion in the middle of the read (pos. 26, starting at 0, C deleted)
3:^snp6-[1-3].*\\s+26M1D34M\\s+.*XE:Z:0:0:SNP:[^:]+:26:[^:]+:C:\\?

$Two deletions in the middle (pos.23 and 27 in the not mutated read): T and C. We don't know how to manage them yet.
s3:^snp7-[1-3].*\\s+23M1D3M1D32M\\s+.*XE:Z:0:0:SNP:[^:]+:23:[^:]+:T:\\?.*XE:Z:0:1:SNP:[^:]+:26:[^:]+:C:\\?

$Two deletions in the middle (pos.23 and 27 in the not mutated read): T and C. We don't know how to manage them yet but we detect that there are several causes.
3:^snp7-[1-3].*\\s+26S32M\\s+.*XE:Z:0:0:BioUndetermined:25:3

$One deletion, on the revcomp, position 27 (T)
3:^snp8-[1-3].*\\s+33M1D27M\\s+.*XE:Z:0:0:SNP:[^:]+:32:[^:]+:A:\\?

$One insertion, middle of the read (position 28, G)
3:^snp9-[1-3].*\\s+28M1I32M\\s+.*XE:Z:0:0:SNP:[^:]+:28:[^:]+:\\?:G

$Deletion, position 24 (G); insertion position 49 (t); substitution position 75 (T -> a); insertion position 98 (a)
3:^snp10-[1-3].*\\s+(23M1D26M1I25M1X22M1I22M|23M1D26M1I48M1I22M)\\s+.*XC:i:4.*XE:Z:0:0:SNP:[^:]+:23:[^:]+:G:\\?.*;1:1:SNP:[^:]+:49:[^:]+:\\?:T.*;2:2:SNP:[^:]+:75:[^:]+:T:A.*;3:3:SNP:[^:]+:98:[^:]+:\\?:A

$ Substitution at 5bp from the last nucleotide of the read (A -> g). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
3:^snp11-[1-3].*\\s+chr1\\s+721\\s+.*\\s+(60M|54M1.5M)\\s+.*XE:Z:0:0:SNP:[^:]+:54:[^:]+:A:G

$ Revcomp of snp11
3:^snp11-rc-[1-3].*\\s+chr1\\s+721\\s+.*\\s+(60M|54M1.5M)\\s+.*XE:Z:0:0:SNP:[^:]+:54:[^:]+:A:G

$ Substitution at 5bp from the first nucleotide of the read (A -> g). CRAC must be launched with --deep-snv --nb-nucleotides-snv-comparison 3
3:^snp12-[1-3].*\\s+chr1\\s+781\\s+.*\\s+(60M|5M1.54M)\\s+.*XE:Z:0:0:SNP:[^:]+:5:[^:]+:A:G

$ Revcomp of snp12
3:^snp12-rc-[1-3].*\\s+chr1\\s+781\\s+.*\\s+(60M|5M1.54M)\\s+.*XE:Z:0:0:SNP:[^:]+:5:[^:]+:A:G
