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  is($annot->{blocks}[0]->{end},567);
  is($annot->{blocks}[0]->{ref_start},1000);
  is($annot->{blocks}[0]->{ref_end},1567);
  is($annot->{blocks}[1]->{size},488);
  is($annot->{blocks}[1]->{start},3512);
  is($annot->{blocks}[1]->{end},4000);
  is($annot->{blocks}[1]->{ref_start},4512);
  is($annot->{blocks}[1]->{ref_end},5000);
  is($annot->{seek_pos},0);
}

# __VCF__ => vcfFileIterator
{

  my $vcf_file = new File::Temp( SUFFIX => '.vcf', UNLINK => 1);
  while(<VCF>) {print $vcf_file $_;}
  close $vcf_file;

  my $vcf_it = CracTools::Utils::vcfFileIterator($vcf_file);
  my $mutation = $vcf_it->();
  is($mutation->{chr},"20");
  is($mutation->{pos},14370);
  is($mutation->{id},"rs6054257");
  is($mutation->{ref},'G');
  is($mutation->{alt}[0],'A');
  is($mutation->{alt}[1],'C');
  is($mutation->{qual},29);
  is($mutation->{filter},'PASS');
  is($mutation->{info}->{NS},3);
  is($mutation->{info}->{DP},14);
  is($mutation->{info}->{AF},0.5);
}

# parseSAMLineLite
{
  my $sam_line = "HWI-ST225:407:C0KV8ACXX:1:1101:2576:2209\t161\t17\t41594644\t254\t45M2807N56M\t17\t41597762\t0\tCGGAAATCCAGAGAACCAACTTAGCAAGCACAGTGCTGTCACTCAAGGCCATGGGTATCAATGATCTGCTGTCCTTTGATTTCATGGATGCCCCACCTATG\t".'@B@FDFDFGHDHDBEE=EBFGGIJCHIEGG...
  my $parsed_line =CracTools::Utils::parseSAMLineLite($sam_line);
  #print STDERR Dumper($parsed_line);
}

# parseCigarChain
{
  my $cigar_chain = "12S5M1X2I3M";
  my @cigar = @{CracTools::Utils::parseCigarChain($cigar_chain)};
  is(@cigar, 5);
  is($cigar[0]->{op}, 'S');
  is($cigar[0]->{nb}, 12);
  is($cigar[1]->{op}, 'M');
  is($cigar[1]->{nb},  5);
  is($cigar[2]->{op}, 'X');
  is($cigar[2]->{nb},  1);
  is($cigar[3]->{op}, 'I');
  is($cigar[3]->{nb},  2);
  is($cigar[4]->{op}, 'M');
  is($cigar[4]->{nb},  3);
}

# Encoding in Base64
{
  my $encoded_list = CracTools::Utils::encodePosListToBase64(1,3,5,8,12,32);
  my @decoded_list = CracTools::Utils::decodePosListInBase64($encoded_list);
  is(@decoded_list,6);
  is($decoded_list[0],1);
  is($decoded_list[1],3);
  is($decoded_list[2],5);
  is($decoded_list[3],8);
  is($decoded_list[4],12);
  is($decoded_list[5],32);
}


__FASTQ__
@HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1
TTAATTGGTAAATAAATCTCCTAATAGCTTAGATNTTACCTTNNNNNNNNNNTAGTTTCTTGAGATTTGTTGGGGGAGACATTTTTGTGATTGCCTTGAT
+HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1
efcfffffcfeefffcffffffddf`feed]`]_Ba_^__[YBBBBBBBBBBRTT\]][]dddd`ddd^dddadd^BBBBBBBBBBBBBBBBBBBBBBBB
@SRR1107833.1 DHCDZDN1:5:1101:1102:1069 length=101
GTGGGGAAGGATCGCAGGCGAGATTACGAGGCGAGGCTCGCGCGCCCGCCCCCGCCCTGGCCCCCAGTGCCCACCCGGTCGGCCCGGCACAGCCATGATCA
+SRR1107833.1 DHCDZDN1:5:1101:1102:1069 length=101
@@CFFFDAHHDHHGGBEEAFGGHHIJCD?DG6FG<ADDE;8'2,59505<57950795A?88A;;08>C::A><>>59)50935<509<B??1?BA:>>3:
__FASTA__
>HSBGPG
GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT
>HSGLTH1
CTTCTTGCCGTGCTCTCTCGAGGTCAGGACGCGAGAGGAAGGCGC
>HDJEJA
ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC
__FASTALONG__
>HSBGPG Human gene for bone gla protein (BGP)
GGCAGATTCCCCCTAGACC
ATAAACAGTGCTGGAGGCT
CTCCAGGCACCCTTCTTTC
ATCCCAGCTGC
>HSGLTH1 Human theta 1-globin gene
CCACTGCACTCACCGCACCCG
CGGGGGGCCTTGGATCCAGGG
CTTCTTGCCGT
__FASTQ_1__
@PAN_0059_FC62WP0AAXX:1:1:1107:937#0/1
GCAGGCGTCCACGGAGTCCAGGCGGGCCGGCAGCTCACGGCCGGCACCCGGGTGCTGGCTGATCACCTCCGCCGC
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@PAN_0059_FC62WP0AAXX:1:1:1350:944#0/1
GGAGATTGAGAAGAGGAAGCAAGGGTAGCCAAATGTGATTCAGTTAATGCGAGAGGTGCTTGTGCATTTTTAGAG
+
KKKIOPQQQ____________W__WXXXWWWWTWVVVSVWWTWW_____YYYYYWWWWWb__bbYYWVY______
__FASTQ_2__
@PAN_0059_FC62WP0AAXX:1:1:1107:937#0/2
AGGTGGCTGTGCAAATAACTGATGTGGCCAGCTTCGTGCCCAGGGACGGGGTGCTGGACGGGGAGGCGCGCAGGCA
+
d_b[e]cfcccaaLacJZ\daede`ffcSaYaac^aaKKLdScaRf_^f_^J_ZdX`BBBBBBBBBBBBBBBBBBB
@PAN_0059_FC62WP0AAXX:1:1:1350:944#0/2
TGCTTGTAGAATATGACTTACCAGCACTCCTGGACCAAGAGCTCTTTGAGTTACTTTTTAATTGGTCCATGTCTCT
+
dhhhhhhhfhhahchhhhcfgghhhhhfhhfa_afhhhhaghhghhaffhhffhhf]fdfhhhhgafhdfhhhhhg
__GFF3__
##gff-version 3
# The organism is Homo Sapiens
# The API version used is 73
HSCHR6_MHC_MANN	Ensembl_CORE	gene	30051790	30051922	.	-	.	ID=ENSG00000266142;Name=CT009552.1;transcripts_nb=1;exons_nb=1
HSCHR6_MHC_MANN	Ensembl_CORE	mRNA	30051790	30051922	.	-	.	ID=ENST00000578939;Parent=ENSG00000266142;exons_nb=1;type=small_ncRNA:miRNA
HSCHR6_MHC_MANN	Ensembl_CORE	exon	30051790	30051922	.	-	.	ID=ENSE00002706393;Parent=ENST00000578939;exon_rank=1
HSCHR6_MHC_MANN	Ensembl_CORE	gene	30068180	30077657	.	+	.	ID=ENSG00000237050;Name=TRIM31-AS1;transcripts_nb=1;exons_nb=4
HSCHR6_MHC_MANN	Ensembl_CORE	mRNA	30068180	30077657	.	+	.	ID=ENST00000412479;Parent=ENSG00000237050;exons_nb=4;type=other_lncRNA:processed_transcript
HSCHR6_MHC_MANN	Ensembl_CORE	exon	30068180	30068327	.	+	.	ID=ENSE00001672229;Parent=ENST00000412479;exon_rank=1
HSCHR6_MHC_MANN	Ensembl_CORE	exon	30077504	30077657	.	+	.	ID=ENSE00001649832;Parent=ENST00000412479;exon_rank=2
HSCHR6_MHC_MANN	Ensembl_CORE	exon	30070604	30070728	.	+	.	ID=ENSE00001723795;Parent=ENST00000412479;exon_rank=3
HSCHR6_MHC_MANN	Ensembl_CORE	exon	30074651	30074772	.	+	.	ID=ENSE00001734310;Parent=ENST00000412479;exon_rank=4