bio-samtools 0.6.2 → 2.0.3
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- checksums.yaml +4 -4
- data/Gemfile +3 -2
- data/README.md +4 -7
- data/VERSION +1 -1
- data/bio-samtools.gemspec +47 -105
- data/doc/Bio.html +68 -131
- data/doc/Bio/DB.html +51 -111
- data/doc/Bio/DB/Alignment.html +135 -363
- data/doc/Bio/DB/Pileup.html +183 -170
- data/doc/Bio/DB/SAM.html +1396 -820
- data/doc/Bio/DB/SAM/Library.html +73 -123
- data/doc/Bio/DB/SAM/Tools.html +51 -273
- data/doc/Bio/DB/Tag.html +78 -124
- data/doc/Bio/DB/Vcf.html +111 -147
- data/doc/LICENSE_txt.html +113 -148
- data/doc/created.rid +9 -10
- data/doc/fonts.css +167 -0
- data/doc/fonts/Lato-Light.ttf +0 -0
- data/doc/fonts/Lato-LightItalic.ttf +0 -0
- data/doc/fonts/Lato-Regular.ttf +0 -0
- data/doc/fonts/Lato-RegularItalic.ttf +0 -0
- data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
- data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/index.html +48 -54
- data/doc/js/darkfish.js +9 -22
- data/doc/js/search.js +20 -5
- data/doc/js/search_index.js +1 -1
- data/doc/rdoc.css +255 -218
- data/doc/table_of_contents.html +256 -137
- data/ext/Rakefile +57 -0
- data/lib/bio-samtools.rb +7 -2
- data/lib/bio/BIOExtensions.rb +89 -0
- data/lib/bio/db/alignment.rb +59 -0
- data/lib/bio/db/fastadb.rb +255 -0
- data/lib/bio/db/pileup.rb +221 -172
- data/lib/bio/db/sam.rb +639 -589
- data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
- data/lib/bio/db/vcf.rb +69 -68
- data/test/.gitignore +1 -0
- data/test/{test_basic.rb → old_test_basic.rb} +33 -1
- data/test/samples/small/dupes.bam +0 -0
- data/test/samples/small/dupes.sam +274 -0
- data/test/samples/small/map_for_reheader.sam +8 -0
- data/test/samples/small/map_to_merge1.bam +0 -0
- data/test/samples/small/map_to_merge1.bam.bai +0 -0
- data/test/samples/small/map_to_merge1.sam +8 -0
- data/test/samples/small/map_to_merge2.bam +0 -0
- data/test/samples/small/map_to_merge2.bam.bai +0 -0
- data/test/samples/small/map_to_merge2.sam +8 -0
- data/test/samples/small/no_md.sam +8 -0
- data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
- data/test/samples/small/test_cov.svg +273 -0
- data/test/samples/small/testu.bam.bai +0 -0
- data/test/svg +133 -0
- data/test/test_pileup.rb +84 -0
- data/test/test_sam.rb +331 -0
- data/test/test_vcf.rb +11 -0
- data/{doc → tutorial}/tutorial.html +0 -0
- data/{doc → tutorial}/tutorial.pdf +0 -0
- metadata +56 -114
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
- data/doc/Bio/DB/SAMException.html +0 -205
- data/doc/LibC.html +0 -155
- data/doc/Pileup.html +0 -571
- data/doc/Vcf.html +0 -473
- data/doc/basic_styles.css +0 -31
- data/doc/classes/Bio.html +0 -139
- data/doc/classes/Bio/DB.html +0 -137
- data/doc/classes/Bio/DB/Alignment.html +0 -441
- data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
- data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
- data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
- data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
- data/doc/classes/Bio/DB/SAM.html +0 -510
- data/doc/classes/Bio/DB/SAM/Library.html +0 -135
- data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
- data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
- data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
- data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
- data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
- data/doc/classes/Bio/DB/SAMException.html +0 -140
- data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
- data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
- data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
- data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
- data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
- data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
- data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
- data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
- data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
- data/doc/classes/Bio/DB/Tag.html +0 -160
- data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
- data/doc/classes/LibC.html +0 -105
- data/doc/classes/Pileup.html +0 -374
- data/doc/classes/Pileup.src/M000001.html +0 -34
- data/doc/classes/Pileup.src/M000002.html +0 -21
- data/doc/classes/Pileup.src/M000003.html +0 -21
- data/doc/classes/Pileup.src/M000004.html +0 -21
- data/doc/classes/Pileup.src/M000005.html +0 -31
- data/doc/files/lib/bio-samtools_rb.html +0 -109
- data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
- data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
- data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
- data/doc/files/lib/bio/db/sam_rb.html +0 -111
- data/doc/fr_class_index.html +0 -43
- data/doc/fr_file_index.html +0 -33
- data/doc/fr_method_index.html +0 -58
- data/doc/lib/bio-samtools_rb.html +0 -115
- data/doc/lib/bio/db/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/bam_rb.html +0 -121
- data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
- data/doc/lib/bio/db/sam/library_rb.html +0 -115
- data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/sam_rb.html +0 -121
- data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
- data/doc/lib/bio/db/sam_rb.html +0 -115
- data/doc/lib/bio/db/vcf_rb.html +0 -124
- data/doc/rdoc-style.css +0 -208
- data/lib/bio/db/sam/bam.rb +0 -210
- data/lib/bio/db/sam/sam.rb +0 -86
- data/test/samples/pipe_char/test.bam +0 -0
- data/test/samples/pipe_char/test.bam.bai +0 -0
- data/test/samples/pipe_char/test.tam +0 -10
- data/test/samples/pipe_char/test_chr.fasta +0 -1000
- data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
- data/test/samples/small/test +0 -0
- data/test/samples/small/test.bam +0 -0
- data/test/samples/small/test.fa +0 -20
- data/test/samples/small/test.fai +0 -0
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@HD VN:1.0 SO:unsorted
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@SQ SN:chr_2 LN:69930
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@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
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test_1 0 chr_2 225 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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test_2 0 chr_2 73 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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reverse_2 16 chr_2 49 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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test_1_SNP 0 chr_2 231 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:28C41 YT:Z:UU
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test_1_DEL 0 chr_2 183 1 27M1D42M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:27^C42 YT:Z:UU
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@SQ SN:chr_1 LN:69930
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@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
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test_1 0 chr_1 225 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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test_2 0 chr_1 73 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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reverse_2 16 chr_1 49 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU
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test_1_SNP 0 chr_1 231 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:28C41 YT:Z:UU
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test_1_DEL 0 chr_1 183 1 27M1D42M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:27^C42 YT:Z:UU
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@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
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test_1_INS 0 chr_1 69 1 29M1I41M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCNCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:70 YT:Z:UU
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reverse_2_SNP 16 chr_1 103 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:34A35 YT:Z:UU
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reverse_2_DEL 16 chr_1 19 1 33M1D36M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:33^A36 YT:Z:UU
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reverse_2_ins 16 chr_1 97 1 35M1I35M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:70 YT:Z:UU
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test_1_SNP_FIRST 0 chr_1 177 1 70M * 0 0 CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0T69 YT:Z:UU
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@PG ID:bowtie2 PN:bowtie2 VN:2.1.0
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test_1 0 chr_1 225 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 YT:Z:UU
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test_2 0 chr_1 73 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 YT:Z:UU
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reverse_2 16 chr_1 49 1 70M * 0 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 YT:Z:UU
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test_1_SNP 0 chr_1 231 1 70M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 YT:Z:UU
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test_1_DEL 0 chr_1 183 1 27M1D42M * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 YT:Z:UU
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