| Previous changeset 8:583abf29fc8e (2017-05-09) Next changeset 10:8da515fbc1bf (2021-09-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2 |
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modified:
macros.xml samtools_mpileup.xml test-data/samtools_mpileup_out_1.pileup test-data/samtools_mpileup_out_3.pileup |
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added:
test-data/mpileup.1.bam test-data/mpileup.2.bam test-data/mpileup.3.bam test-data/mpileup.out.1 test-data/mpileup.out.3 test-data/mpileup.ref.fa test-data/mpileup.ref.fa.fai test-data/phiX.fasta.fai test-data/samtools_mpileup_out_2.pileup |
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removed:
test-data/samtools_mpileup_out_2.vcf |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a macros.xml --- a/macros.xml Tue May 09 11:17:20 2017 -0400 +++ b/macros.xml Mon Sep 03 13:10:02 2018 -0400 |
| [ |
| @@ -1,11 +1,45 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.3.1</token> + <token name="@TOOL_VERSION@">1.9</token> + <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ + ##prepare input and indices + #for $i, $bam in enumerate( $input_bams ): + ln -s '$bam' '${i}' && + #if $bam.is_of_type('bam'): + #if str( $bam.metadata.bam_index ) != "None": + ln -s '${bam.metadata.bam_index}' '${i}.bai' && + #else: + samtools index '${i}' '${i}.bai' && + #end if + #elif $bam.is_of_type('cram'): + #if str( $bam.metadata.cram_index ) != "None": + ln -s '${bam.metadata.cram_index}' '${i}.crai' && + #else: + samtools index '${i}' '${i}.crai' && + #end if + #end if + #end for + ]]></token> + <xml name="flag_options"> + <option value="1">read is paired</option> + <option value="2">read is mapped in a proper pair</option> + <option value="4">read is unmapped</option> + <option value="8">mate is unmapped</option> + <option value="16">read reverse strand</option> + <option value="32">mate reverse strand</option> + <option value="64">read is the first in a pair</option> + <option value="128">read is the second in a pair</option> + <option value="256">alignment or read is not primary</option> + <option value="512">read fails platform/vendor quality checks</option> + <option value="1024">read is a PCR or optical duplicate</option> + <option value="2048">supplementary alignment</option> + </xml> <xml name="citations"> <citations> <citation type="bibtex"> |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a samtools_mpileup.xml --- a/samtools_mpileup.xml Tue May 09 11:17:20 2017 -0400 +++ b/samtools_mpileup.xml Mon Sep 03 13:10:02 2018 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_mpileup" name="MPileup" version="2.1.3">\n+<tool id="samtools_mpileup" name="samtools mpileup" version="2.1.4">\n <description>multi-way pileup of variants</description>\n <macros>\n <import>macros.xml</import>\n@@ -7,10 +7,9 @@\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command><![CDATA[\n- #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):\n- ln -s \'${input_bam}\' \'localbam_${bam_count}.bam\' &&\n- ln -s \'${input_bam.metadata.bam_index}\' \'localbam_${bam_count}.bam.bai\' &&\n- #end for\n+ \n+ #set $input_bams = $reference_source.input_bam\n+ @PREPARE_IDX_MULTIPLE@\n \n #if $reference_source.reference_source_selector == "history":\n ln -s \'${reference_source.ref_file}\' &&\n@@ -23,28 +22,38 @@\n #else:\n -f \'${reference_source.ref_file}\'\n #end if\n- #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):\n- localbam_${bam_count}.bam\n+ #for $i in range(len( $input_bams )):\n+ \'${i}\'\n #end for\n+\n #if str( $advanced_options.advanced_options_selector ) == "advanced":\n #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":\n #if $advanced_options.filter_by_flags.require_flags:\n- --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(\',\')])}\n+ #set $filter = $advanced_options.filter_by_flags.require_flags\n+ @FLAGS@\n+ --rf $flags\n #end if\n #if $advanced_options.filter_by_flags.exclude_flags:\n- --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(\',\')])}\n+ #set $filter = $advanced_options.filter_by_flags.exclude_flags\n+ @FLAGS@\n+ --ff $flags\n #end if\n #end if\n- #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":\n- -l \'$pasted_regions\'\n- #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"\n- -l \'$advanced_options.limit_by_region.bed_regions\'\n+ #if str($advanced_options.limit_by_region.limit_by_regions) == "limit":\n+ #if str( $advanced_options.limit_by_region.region_paste ) != "None":\n+ -r \'$advanced_options.limit_by_region.region_paste\'\n+ #end if\n+ #if str( $advanced_options.limit_by_region.bed_regions ) != "None"\n+ -l \'$advanced_options.limit_by_region.bed_regions\'\n+ #end if\n #end if\n+ \n #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n -G \'$excluded_read_groups\'\n #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"\n -G \'$advanced_options.exclude_read_group.read_groups\'\n #end if\n+ ${advanced_options.ignore_overlaps}\n ${advanced_options.skip_anomalous_read_pairs}\n ${advanced_options.disable_probabilistic_realignment}\n -C ${advanced_options.coefficient_for_downgrading}\n@@ -52,60 +61,16 @@\n ${advanced_options.extended_BAQ_computation}\n -q ${advanced_options.minimum_mapping_quality}\n -Q ${advanced_options.minimum_base_quality}\n- #if str( $advanced_options.region_string ):\n- -r \'${advanced_options.region_string}\'\n- #end if\n+ $advanced_options.qualities_illumina_onethree\n #end if\n- #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == \'perform_genotype_likelihood_computation\':\n- ${genotype_likelihood_computation_type.output_format}\n- ${genotype_likelihood_computation_type.compressed}\n-\n- #if str( $genotype_likelihood_computation_type.output_tags ) != "None":\n- --output-tags \'${genotype_likelihood_computation_type.output_tags}\'\n- #end if'..b' file="samtools_mpileup_out_3.pileup" />\n+ <conditional name="output_options_cond">\n+ <param name="output_options_cond" value="advanced" />\n+ <param name="base_position_on_reads" value="true" />\n+ <param name="output_mapping_quality" value="true" />\n+ </conditional>\n+ <conditional name="advanced_options">\n+ <param name="advanced_options_selector" value="advanced" />\n+ <param name="minimum_base_quality" value="0" /><!-- most reads have ultra low quality resuling in empty columns -->\n+ </conditional>\n+ <output name="output_file_pu" file="samtools_mpileup_out_3.pileup" ftype="pileup" />\n </test>\n </tests>\n <help><![CDATA[\n **What it does**\n \n-Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines.\n-If sample identifiers are absent, each input file is regarded as one sample.\n+Generate pileup for one or multiple BAM files. Alignment records are grouped by sample (SM) identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.\n+\n+Generation of VCF and BCF output, is deprecated and not available in the Galaxy tool. Please use bcftools mpileup for this instead.\n+\n+In the pileup format (without -u or -g), each line represents a genomic position, consisting of chromosome name, 1-based coordinate, reference base, the number of reads covering the site, read bases, base qualities and alignment mapping qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a \'>\' or \'<\' for a reference skip, \'ACGTN\' for a mismatch on the forward strand and \'acgtn\' for a mismatch on the reverse strand. A pattern \'\\\\+[0-9]+[ACGTNacgtn]+\' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Similarly, a pattern \'-[0-9]+[ACGTNacgtn]+\' represents a deletion from the reference. The deleted bases will be presented as \'*\' in the following lines. Also at the read base column, a symbol \'^\' marks the start of a read. The ASCII of the character following \'^\' minus 33 gives the mapping quality. A symbol \'$\' marks the end of a read segment.\n+\n+Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file. \n \n-**Notes**: Assuming diploid individuals.\n+**BAQ (Base Alignment Quality)**\n+\n+BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper \xe2\x80\x9cImproving SNP discovery by base alignment quality\xe2\x80\x9d, Heng Li, Bioinformatics, Volume 27, Issue 8 <https://doi.org/10.1093/bioinformatics/btr076>\n+\n+BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.\n+\n+It is possible to store pre-calculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment. \n ]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.1.bam |
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| Binary file test-data/mpileup.1.bam has changed |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.2.bam |
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| Binary file test-data/mpileup.2.bam has changed |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.3.bam |
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| Binary file test-data/mpileup.3.bam has changed |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.out.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.out.1 Mon Sep 03 13:10:02 2018 -0400 |
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| @@ -0,0 +1,51 @@ +17 100 C 9 ......... JLJMLLGG4 3 ... DmH 5 ..... HIJ?G +17 101 C 9 ......... HFLJKMH97 3 ... Aq5 5 ..... FEIEG +17 102 C 9 ......... FKKLLLKF5 3 ... GpA 5 ..... HHIJG +17 103 T 8 ........ KLLLMLKG 3 ... Fu; 5 ..... MIMHI +17 104 G 8 ........ ;HLGKLIH 2 .. Dp 5 ..... ICHCI +17 105 G 9 ........^]. HB6KKKG8; 3 ... Cj0 5 ..... GBCAH +17 106 G 10 .......... GMKKIKJE2> 2 .. @i 5 ..... GCF5J +17 107 C 9 ......... IKMKLJKI? 3 ... Gm; 5 ..... JGH?K +17 108 C 9 ......... HGKLLKLG? 3 ... Fq< 5 ..... IFGBK +17 109 T 9 ......... ILLOLJJFB 3 ... FvI 5 ..... JJMLL +17 110 G 9 ......... JJMMKLIHD 3 ... ?t? 5 ..... IDFII +17 111 G 10 .......... G77HJJBA/C 2 .. Cr 4 .... GCHK +17 112 C 9 ......... IKILKKLI? 3 ... 6t; 5 ..... J?IEJ +17 113 A 9 ......... CGIFIGJE? 2 .. Bs 5 ..... JBJJI +17 114 C 9 ......... IDGIJJIHB 3 ... Ar; 5 ..... GEDHI +17 115 C 10 .......... EJJILNGF/A 2 .. Ds 6 .....^]. HFHIH? +17 116 A 9 ......... DHGJJJIHF 2 .. Ev 7 ......, F8JGIGG +17 117 G 9 .$........ >BJIMIFJF 2 .. @t 7 ......, H>IFJDD +17 118 G 9 ......... BFKLJGF/A 1 . s 7 ......, A>CEECE +17 119 G 8 ........ F?HLKJGG 2 .. s1 7 ......, A1ABLCB +17 120 A 8 ........ FCIIKHGJ 2 .. w= 7 ......, E;I@GIE +17 121 G 8 ........ GFMMMG@H 2 .. u9 7 ......, A<DBJGB +17 122 C 8 .$....... DEIKLLJI 3 ..^]. u2C 7 .$....., E=JGKFH +17 123 T 7 ....... EMKIEFH 3 ... y>I 6 ....., EJ;LKK +17 124 T 9 .$.......^]. ?HEIE?/7> 3 ... q6F 6 ....., ?FBCGI +17 125 A 7 ....... DHICDGA 3 ... s6F 6 ....., CIBHFD +17 126 A 8 ........ JEKAG0GB 3 ... p6I 6 ....., GHEMKC +17 127 C 8 ........ JGGJG/DD 3 ... p@E 6 ....., ?GDHGI +17 128 A 8 ........ HJIIE8IE 3 ... rFG 6 .$...., >GGJHF +17 129 A 8 ........ HFKJD8IC 3 ... oCJ 5 ...., IIMKD +17 130 A 8 ......$.. IJKCE8JD 3 ... kHJ 5 ...., BEMKI +17 131 C 7 ....... JKKFGGG 3 ... jCF 5 ...., BDKHF +17 132 A 7 ....... JGKJGKF 3 .$.. nIF 5 ...., HGJGG +17 133 T 7 ....... GKHIEGE 3 .,. ELH 5 ...., EGJIK +17 134 C 7 ....... KLMKKJH 3 .,. IKI 5 ...., EGJKD +17 135 T 7 ....... JLKLHIG 3 .,. HJK 5 .$..., DLLJ? +17 136 G 7 ....... IMLGIHH 3 .,. HKI 5 ...,^]. ;FIE@ +17 137 T 7 ....... EJHHAHF 3 .,. IKH 5 ...,. FGIH: +17 138 C 7 ....... GKMIJIH 3 .,. ILK 5 ...,. GHKA9 +17 139 C 7 ....... FJK@GFF 3 .,. CKJ 5 ...,. FLG>< +17 140 A 7 .$...... CIIKFHF 3 .,. GMI 5 ...,. IKJBE +17 141 G 6 ...... MLCJEJ 3 .,. DLK 5 ...,. ;MHAC +17 142 C 6 ...... LLFIHF 3 .,. CBJ 5 ...,. AFI;6 +17 143 G 6 ...... CAE@B@ 3 .,. :KB 4 ..., 3?AG +17 144 A 6 ...... JJJGBG 3 .,. GJJ 5 ...,. 7LCJ< +17 145 A 6 ...... IJCGKG 3 .,. DIL 5 ...,. <MKH9 +17 146 T 6 ...... HJJFFG 3 .,. GII 5 ...,. ?JFI0 +17 147 A 6 ...... FIJEID 3 .,. FEI 5 ...,. FKGA9 +17 148 C 6 ...... KKJGHG 3 .,. DKJ 5 ...,. GHHBC +17 149 C 6 ...... JL3IGH 3 .$,. ?LL 5 ...,. EICE@ +17 150 T 6 ...... KJIEEH 2 ,. IM 5 ...,. LIKG? |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.out.3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.out.3 Mon Sep 03 13:10:02 2018 -0400 |
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| @@ -0,0 +1,11 @@ +17 1050 A 6 .$..... DGIKIF +17 1051 A 5 ..... HFJHD +17 1052 A 5 ..... BIKJB +17 1053 A 5 ..... GFJGB +17 1054 C 5 ..... I@JHB +17 1055 C 7 .....^].^]. HKNK9@A +17 1056 C 7 ....... HKMK7A@ +17 1057 T 7 ....... JDKJDGF +17 1058 G 7 ....... HHLKHIH +17 1059 T 7 ....... EHII?EE +17 1060 C 7 ....... JJJI=GH |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.ref.fa Mon Sep 03 13:10:02 2018 -0400 |
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| @@ -0,0 +1,71 @@ +>17 17:1-4200 +AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA +TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA +GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA +GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC +GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA +GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA +AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA +AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG +GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC +ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG +TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT +GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG +CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA +AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA +TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC +CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG +TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG +CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA +GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC +CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT +TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC +CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC +GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC +CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA +GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA +GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT +TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC +CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG +CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA +CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC +TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG +TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA +GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC +CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC +GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC +AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC +ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG +GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG +CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC +GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA +AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG +AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG +CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA +ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG +CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT +CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT +TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG +ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG +TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT +TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG +CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG +CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG +ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG +GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA +ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA +GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG +GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG +GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT +AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC +TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT +ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG +TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC +ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC +CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG +TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT +GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT +GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT +ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT +TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT +CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/mpileup.ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.ref.fa.fai Mon Sep 03 13:10:02 2018 -0400 |
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| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/phiX.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta.fai Mon Sep 03 13:10:02 2018 -0400 |
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| @@ -0,0 +1,1 @@ +phiX174 5386 9 70 71 |
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| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/samtools_mpileup_out_1.pileup --- a/test-data/samtools_mpileup_out_1.pileup Tue May 09 11:17:20 2017 -0400 +++ b/test-data/samtools_mpileup_out_1.pileup Mon Sep 03 13:10:02 2018 -0400 |
| b |
| @@ -1,43 +1,43 @@ -phiX174 1411 A 0 -phiX174 1412 G 0 -phiX174 1413 C 0 -phiX174 1414 G 0 -phiX174 1415 C 0 -phiX174 1416 C 0 -phiX174 1417 G 0 -phiX174 1418 T 0 -phiX174 1419 G 0 -phiX174 1420 G 0 -phiX174 1421 A 0 -phiX174 1422 T 0 -phiX174 1423 G 0 -phiX174 1424 C 0 -phiX174 1425 C 0 -phiX174 1426 T 0 -phiX174 1427 G 0 -phiX174 1428 A 0 -phiX174 1429 C 0 -phiX174 1430 C 0 -phiX174 1431 G 0 -phiX174 1432 T 0 -phiX174 1433 A 0 -phiX174 1434 C 0 -phiX174 1435 C 0 -phiX174 1436 G 0 -phiX174 1437 A 0 -phiX174 1438 G 0 -phiX174 1439 G 0 -phiX174 1440 C 0 -phiX174 1441 T 0 -phiX174 1442 A 0 -phiX174 1443 A 0 -phiX174 1444 C 0 -phiX174 1445 C 0 -phiX174 1446 C 0 -phiX174 1447 T 0 -phiX174 1448 A 0 -phiX174 1449 A 0 -phiX174 1450 T 0 -phiX174 1451 G 0 -phiX174 1452 A 0 -phiX174 1453 G 0 +phiX174 1411 A 0 * * * * +phiX174 1412 G 0 * * * * +phiX174 1413 C 0 * * * * +phiX174 1414 G 0 * * * * +phiX174 1415 C 0 * * * * +phiX174 1416 C 0 * * * * +phiX174 1417 G 0 * * * * +phiX174 1418 T 0 * * * * +phiX174 1419 G 0 * * * * +phiX174 1420 G 0 * * * * +phiX174 1421 A 0 * * * * +phiX174 1422 T 0 * * * * +phiX174 1423 G 0 * * * * +phiX174 1424 C 0 * * * * +phiX174 1425 C 0 * * * * +phiX174 1426 T 0 * * * * +phiX174 1427 G 0 * * * * +phiX174 1428 A 0 * * * * +phiX174 1429 C 0 * * * * +phiX174 1430 C 0 * * * * +phiX174 1431 G 0 * * * * +phiX174 1432 T 0 * * * * +phiX174 1433 A 0 * * * * +phiX174 1434 C 0 * * * * +phiX174 1435 C 0 * * * * +phiX174 1436 G 0 * * * * +phiX174 1437 A 0 * * * * +phiX174 1438 G 0 * * * * +phiX174 1439 G 0 * * * * +phiX174 1440 C 0 * * * * +phiX174 1441 T 0 * * * * +phiX174 1442 A 0 * * * * +phiX174 1443 A 0 * * * * +phiX174 1444 C 0 * * * * +phiX174 1445 C 0 * * * * +phiX174 1446 C 0 * * * * +phiX174 1447 T 0 * * * * +phiX174 1448 A 0 * * * * +phiX174 1449 A 0 * * * * +phiX174 1450 T 0 * * * * +phiX174 1451 G 0 * * * * +phiX174 1452 A 0 * * * * +phiX174 1453 G 0 * * * * |
| b |
| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/samtools_mpileup_out_2.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_mpileup_out_2.pileup Mon Sep 03 13:10:02 2018 -0400 |
| b |
| b'@@ -0,0 +1,5385 @@\n+phiX174\t2\tA\t1\t^K.\t2\n+phiX174\t3\tG\t2\t.^K.\t22\n+phiX174\t4\tT\t4\t..^K.^K.\t2222\n+phiX174\t5\tT\t6\t....^K.^K.\t222222\n+phiX174\t6\tT\t6\t......\t222222\n+phiX174\t7\tT\t8\t......^K.^K.\t22222222\n+phiX174\t8\tA\t9\t........^K.\t222222222\n+phiX174\t9\tT\t10\t.........^K.\t2222222222\n+phiX174\t10\tC\t10\t..........\t2222222222\n+phiX174\t11\tG\t13\t..........^K.^K.^K.\t2222222222222\n+phiX174\t12\tC\t14\t.............^K.\t22222222222222\n+phiX174\t13\tT\t15\t..............^K.\t222222222222222\n+phiX174\t14\tT\t16\t...............^K.\t2222222222222222\n+phiX174\t15\tC\t16\t.........G......\t2222222222222222\n+phiX174\t16\tC\t18\t................^K.^K.\t222222222222222222\n+phiX174\t17\tA\t22\t..................^K.^K.^K.^K.\t2222222222222222222222\n+phiX174\t18\tT\t23\t................A.....^K.\t22222222222222222222222\n+phiX174\t19\tG\t23\t.......................\t22222222222222222222222\n+phiX174\t20\tA\t23\t.......................\t22222222222222222222222\n+phiX174\t21\tC\t24\t.......................^K.\t222222222222222222222222\n+phiX174\t22\tG\t27\t........................^K.^K.^K.\t222222222222222222222222222\n+phiX174\t23\tC\t28\t....................G......^K.\t2222222222222222222222222222\n+phiX174\t24\tA\t29\t............................^K.\t22222222222222222222222222222\n+phiX174\t25\tG\t30\t.............................^K.\t222222222222222222222222222222\n+phiX174\t26\tA\t32\t..............................^K.^K.\t22222222222222222222222222222222\n+phiX174\t27\tA\t35\t................................^K.^K.^K.\t22222222222222222222222222222222222\n+phiX174\t28\tG\t35\t...................................\t22222222222222222222222222222222222\n+phiX174\t29\tT\t36\t.............A.....A...............^K.\t222222222222222222222222222222222222\n+phiX174\t30\tT\t37\t.........A........................A.^K.\t2222222222222222222222222222222222222\n+phiX174\t31\tA\t39\t....................................C^K.^K.\t222222222222222222222222222222222222222\n+phiX174\t32\tA\t39\t.......................................\t222222222222222222222222222222222222222\n+phiX174\t33\tC\t40\t.......................................^K.\t2222222222222222222222222222222222222222\n+phiX174\t34\tA\t40\t.C......................................\t2222222222222222222222222222222222222222\n+phiX174\t35\tC\t41\t........................................^K.\t22222222222222222222222222222222222222222\n+phiX174\t36\tT\t41\tA..............A........A................\t22222222222222222222222222222222222222222\n+phiX174\t37\tT\t41\t.........................................\t22222222222222222222222222222222222222222\n+phiX174\t38\tT\t41\t.......................................A.\t22222222222222222222222222222222222222222\n+phiX174\t39\tC\t41\t.........................................\t22222222222222222222222222222222222222222\n+phiX174\t40\tG\t41\t.........................................\t22222222222222222222222222222222222222222\n+phiX174\t41\tG\t42\t.........................................^K.\t222222222222222222222222222222222222222222\n+phiX174\t42\tA\t42\t..........................................\t222222222222222222222222222222222222222222\n+phiX174\t43\tT\t43\tA.........................................^K.\t2222222222222222222222222222222222222222222\n+phiX174\t44\tA\t43\t...............C...........................\t2222222222222222222222222222222222222222222\n+phiX174\t45\tT\t43\t............A..................A...........\t2222222222222222222222222222222222222222222\n+phiX174\t46\tT\t45\t...........................................^K.^K.\t222222222222222222222222222222222222222222222\n+phiX174\t47\tT\t45\t.............................................\t222222222222222222222222222222222222222222222\n+phiX174\t48\tC\t45\t.............................................\t222222222222222222222222222222222222222222222\n+phiX174\t49\tT\t47\t...A.A...............A.......................^K.^K.\t22222222222222222222222222222222222222222222222\n+phiX174\t50\tG\t49\t..........T....................................^K.^K.\t2222222222222222222222222222222222222222222222222\n+phiX174\t51\tA\t50\t.................................................^K.\t22222222222222222222222222222222222222222222222222\n+phiX174\t52\tT\t51\t............................'..b',,,,,,,,,,,,,\t222222222222222222222222222222222222222222222222222222222222\n+phiX174\t5336\tG\t57\t,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,c,,,,,,,,,,,\t222222222222222222222222222222222222222222222222222222222\n+phiX174\t5337\tC\t56\ta,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a,,,,,,,,,,,,,,,\t22222222222222222222222222222222222222222222222222222222\n+phiX174\t5338\tT\t56\t,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222222222222222222222222222\n+phiX174\t5339\tC\t55\t,$,,,,,,,,,,,,,a,,,,,,,,,,,,,,,,,,a,,,,,,,,,,,,,,,,,,,,,\t2222222222222222222222222222222222222222222222222222222\n+phiX174\t5340\tA\t54\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t,,,,,,,,,,,,,,,,,,\t222222222222222222222222222222222222222222222222222222\n+phiX174\t5341\tA\t54\t,,,,,,,,,,,,,,,,,t,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t222222222222222222222222222222222222222222222222222222\n+phiX174\t5342\tA\t54\t,$,$,,,,,,,,,,,,,,,,,,,,,,,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t222222222222222222222222222222222222222222222222222222\n+phiX174\t5343\tT\t52\t,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t2222222222222222222222222222222222222222222222222222\n+phiX174\t5344\tT\t49\t,,,,,,,,,,,,g,,,,,,,,,,,,,,,,,,,,,,,,,,,g,,,,,,,,\t2222222222222222222222222222222222222222222222222\n+phiX174\t5345\tT\t49\t,$,$,$,$,$,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t2222222222222222222222222222222222222222222222222\n+phiX174\t5346\tA\t42\t,$,,,,,,,,,,,t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t222222222222222222222222222222222222222222\n+phiX174\t5347\tT\t41\t,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222222222222\n+phiX174\t5348\tG\t39\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,c,,,,,,,,,,\t222222222222222222222222222222222222222\n+phiX174\t5349\tC\t39\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t222222222222222222222222222222222222222\n+phiX174\t5350\tG\t39\t,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,c,,,,,,,,,\t222222222222222222222222222222222222222\n+phiX174\t5351\tC\t38\t,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222222222\n+phiX174\t5352\tG\t37\t,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t2222222222222222222222222222222222222\n+phiX174\t5353\tC\t35\t,a,,,,,,,,,,,a,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222222\n+phiX174\t5354\tT\t35\t,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222222\n+phiX174\t5355\tT\t33\tg$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t.22222222222222222222222222222222\n+phiX174\t5356\tC\t32\t,,,,,,,,,,,,,,,,a,,,,,,,,,,,,,,,\t22222222222222222222222222222222\n+phiX174\t5357\tG\t32\t,,,c,,,,,,,,,,,,,,,,,,,,,c,,,,,,\t22222222222222222222222222222222\n+phiX174\t5358\tA\t32\t,$,,,,,,,,,,,,t,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222222\n+phiX174\t5359\tT\t31\t,$,$,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t2222222222222222222222222222222\n+phiX174\t5360\tA\t29\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t22222222222222222222222222222\n+phiX174\t5361\tA\t29\t,$t,,,,,,t,,,,,,,,,,,,,,,,,,,,\t2/222222222222222222222222222\n+phiX174\t5362\tA\t28\t,$,,,,,,,,,,,,,,,,,,,,,,,,,,,\t/222222222222222222222222222\n+phiX174\t5363\tA\t27\t,$,$,t,,,,,,,,,,,,,,,,,,,,,,,\t222/22222222222222222222222\n+phiX174\t5364\tA\t25\t,$,$,$,$,,,,,,,,,,,,,,,,,,,,,\t2/22222222222222222222222\n+phiX174\t5365\tT\t21\t,$,,,,,,,,,,,,,,g,,g,,\t222222222222222222222\n+phiX174\t5366\tG\t20\t,$,,c,,,,,,,,,,,,,,,,\t22222222222222222222\n+phiX174\t5367\tA\t19\t,$,,,,,,,,,,,,,,,,,,\t2222222222222222222\n+phiX174\t5368\tT\t18\t,$,$,,,,,,,,,,,,,,,,\t222222222222222222\n+phiX174\t5369\tT\t16\t,,,,,,,,,,,,,,,,\t2222222222222222\n+phiX174\t5370\tG\t16\t,$,$,,,,,,,,,,,,,,\t2222222222222222\n+phiX174\t5371\tG\t14\t,$,$,,,,,,,,,,,c\t22222222222222\n+phiX174\t5372\tC\t12\t,,,,,,,,,,,,\t222222222222\n+phiX174\t5373\tG\t12\t,,,,,,,,,,,,\t022222222222\n+phiX174\t5374\tT\t11\t,,,,,,,,,,,\t22222222222\n+phiX174\t5375\tA\t11\t,$,,,,,,,,,,\t22222222222\n+phiX174\t5376\tT\t10\t,$,,,,,,,,,\t2222222222\n+phiX174\t5377\tC\t9\t,$,$,$,,,,,,\t222222222\n+phiX174\t5378\tC\t6\t,,,,,,\t222222\n+phiX174\t5379\tA\t6\t,,,,,,\t202222\n+phiX174\t5380\tA\t5\t,$,,,,\t22222\n+phiX174\t5381\tC\t4\t,,,,\t2222\n+phiX174\t5382\tC\t4\t,,,,\t2222\n+phiX174\t5383\tT\t4\t,,,,\t2222\n+phiX174\t5384\tG\t4\t,$,$,,\t2222\n+phiX174\t5385\tC\t2\t,$,\t22\n+phiX174\t5386\tA\t1\t,$\t2\n' |
| b |
| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/samtools_mpileup_out_2.vcf --- a/test-data/samtools_mpileup_out_2.vcf Tue May 09 11:17:20 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER=<ID=PASS,Description="All filters passed"> -##samtoolsVersion=1.1+htslib-1.1 -##samtoolsCommand=samtools mpileup --VCF --uncompressed -f /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -g -e 20 -h 100 -L 250 -m 1 --open-prob 40 -F 0.002 -e 40 --output /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_736.dat /tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_734.dat -##reference=file:///tmp/tmpId8vOP/tmp3bubIE/database/files/000/dataset_735.dat -##contig=<ID=phiX174,length=5386> -##ALT=<ID=*,Description="Represents allele(s) other than observed."> -##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> -##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> -##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> -##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> -##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> -##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> -##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> -##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> -##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> -##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> -##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h"> -##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT localbam_0.bam |
| b |
| diff -r 583abf29fc8e -r fa7ad9b89f4a test-data/samtools_mpileup_out_3.pileup --- a/test-data/samtools_mpileup_out_3.pileup Tue May 09 11:17:20 2017 -0400 +++ b/test-data/samtools_mpileup_out_3.pileup Mon Sep 03 13:10:02 2018 -0400 |
| b |
| @@ -1,43 +1,43 @@ -phiX174 1411 A 1 ^P. $ P 1 -phiX174 1412 G 3 .^D.^F. "$$ PDF 2,1,1 -phiX174 1413 C 5 ...^D.^F. """$$ PDFDF 3,2,2,1,1 -phiX174 1414 G 6 .....^F. #####$ PDFDFF 4,3,3,2,2,1 -phiX174 1415 C 7 ......^F. %%%%%%& PDFDFFF 5,4,4,3,3,2,1 -phiX174 1416 C 8 .......^F. $$$$$$$$ PDFDFFFF 6,5,5,4,4,3,2,1 -phiX174 1417 G 9 ........^F. "#######$ PDFDFFFFF 7,6,6,5,5,4,3,2,1 -phiX174 1418 T 10 .........^F. """""""""$ PDFDFFFFFF 8,7,7,6,6,5,4,3,2,1 -phiX174 1419 G 10 .......... """""'&'%$ PDFDFFFFFF 9,8,8,7,7,6,5,4,3,2 -phiX174 1420 G 10 .......... """""""""" PDFDFFFFFF 10,9,9,8,8,7,6,5,4,3 -phiX174 1421 A 10 .......... """""""""" PDFDFFFFFF 11,10,10,9,9,8,7,6,5,4 -phiX174 1422 T 10 .......... """""""""" PDFDFFFFFF 12,11,11,10,10,9,8,7,6,5 -phiX174 1423 G 10 .......... """""""""# PDFDFFFFFF 13,12,12,11,11,10,9,8,7,6 -phiX174 1424 C 10 ..A.AAAAAA %""""""""" PDFDFFFFFF 14,13,13,12,12,11,10,9,8,7 -phiX174 1425 C 10 .......... $$$""""""" PDFDFFFFFF 15,14,14,13,13,12,11,10,9,8 -phiX174 1426 T 10 .......... #####""""" PDFDFFFFFF 16,15,15,14,14,13,12,11,10,9 -phiX174 1427 G 10 .......... ######"""" PDFDFFFFFF 17,16,16,15,15,14,13,12,11,10 -phiX174 1428 A 10 .......... """""""""" PDFDFFFFFF 18,17,17,16,16,15,14,13,12,11 -phiX174 1429 C 10 .......... ((((((&("" PDFDFFFFFF 19,18,18,17,17,16,15,14,13,12 -phiX174 1430 C 10 .......... $$$$$$$$$" PDFDFFFFFF 20,19,19,18,18,17,16,15,14,13 -phiX174 1431 G 10 .......... ########## PDFDFFFFFF 21,20,20,19,19,18,17,16,15,14 -phiX174 1432 T 10 .......... """""""""" PDFDFFFFFF 22,21,21,20,20,19,18,17,16,15 -phiX174 1433 A 10 .......... ########## PDFDFFFFFF 23,22,22,21,21,20,19,18,17,16 -phiX174 1434 C 10 .......... ((((((&(%$ PDFDFFFFFF 24,23,23,22,22,21,20,19,18,17 -phiX174 1435 C 10 .......... $$$$$$$$$$ PDFDFFFFFF 25,24,24,23,23,22,21,20,19,18 -phiX174 1436 G 10 .......... ########## PDFDFFFFFF 26,25,25,24,24,23,22,21,20,19 -phiX174 1437 A 10 .......... """""""""! PDFDFFFFFF 27,26,26,25,25,24,23,22,21,20 -phiX174 1438 G 10 .......... """""####! PDFDFFFFFF 28,27,27,26,26,25,24,23,22,21 -phiX174 1439 G 10 .......... """""""""! PDFDFFFFFF 29,28,28,27,27,26,25,24,23,22 -phiX174 1440 C 10 .......... """""""""! PDFDFFFFFF 30,29,29,28,28,27,26,25,24,23 -phiX174 1441 T 10 .......... """"""""#! PDFDFFFFFF 31,30,30,29,29,28,27,26,25,24 -phiX174 1442 A 10 .......... $$$%%%&&%! PDFDFFFFFF 32,31,31,30,30,29,28,27,26,25 -phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! PDFDFFFFFF 33,32,32,31,31,30,29,28,27,26 -phiX174 1444 C 10 **.*...... !!"!"""""! PDFDFFFFFF 34,33,33,32,32,31,30,29,28,27 -phiX174 1445 C 10 .......... !!&!%%%&%! PDFDFFFFFF 34,33,34,32,33,32,31,30,29,28 -phiX174 1446 C 10 .......... !!"!"""""! PDFDFFFFFF 35,34,35,33,34,33,32,31,30,29 -phiX174 1447 T 10 .$..$....... !!#!"""""! PDFDFFFFFF 36,35,36,34,35,34,33,32,31,30 -phiX174 1448 A 8 .$..$..... !!#%%$$! DDFFFFFF 36,35,36,35,34,33,32,31 -phiX174 1449 A 6 .$.$.... !""""! DFFFFF 36,36,35,34,33,32 -phiX174 1450 T 4 .$... """! FFFF 36,35,34,33 -phiX174 1451 G 3 .$.. #"! FFF 36,35,34 -phiX174 1452 A 2 .$. "! FF 36,35 -phiX174 1453 G 1 .$ ! F 36 +phiX174 1411 A 1 ^P. $ +phiX174 1412 G 3 .^D.^F. "$$ +phiX174 1413 C 5 ...^D.^F. """$$ +phiX174 1414 G 6 .....^F. #####$ +phiX174 1415 C 7 ......^F. %%%%%%& +phiX174 1416 C 8 .......^F. $$$$$$$$ +phiX174 1417 G 9 ........^F. "#######$ +phiX174 1418 T 10 .........^F. """""""""$ +phiX174 1419 G 10 .......... """""'&'%$ +phiX174 1420 G 10 .......... """""""""" +phiX174 1421 A 10 .......... """""""""" +phiX174 1422 T 10 .......... """""""""" +phiX174 1423 G 10 .......... """""""""# +phiX174 1424 C 10 ..A.AAAAAA %""""""""" +phiX174 1425 C 10 .......... $$$""""""" +phiX174 1426 T 10 .......... #####""""" +phiX174 1427 G 10 .......... ######"""" +phiX174 1428 A 10 .......... """""""""" +phiX174 1429 C 10 .......... ((((((&("" +phiX174 1430 C 10 .......... $$$$$$$$$" +phiX174 1431 G 10 .......... ########## +phiX174 1432 T 10 .......... """""""""" +phiX174 1433 A 10 .......... ########## +phiX174 1434 C 10 .......... ((((((&(%$ +phiX174 1435 C 10 .......... $$$$$$$$$$ +phiX174 1436 G 10 .......... ########## +phiX174 1437 A 10 .......... """""""""! +phiX174 1438 G 10 .......... """""####! +phiX174 1439 G 10 .......... """""""""! +phiX174 1440 C 10 .......... """""""""! +phiX174 1441 T 10 .......... """"""""#! +phiX174 1442 A 10 .......... $$$%%%&&%! +phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! +phiX174 1444 C 10 **.*...... !!"!"""""! +phiX174 1445 C 10 .......... !!&!%%%&%! +phiX174 1446 C 10 .......... !!"!"""""! +phiX174 1447 T 10 .$..$....... !!#!"""""! +phiX174 1448 A 8 .$..$..... !!#%%$$! +phiX174 1449 A 6 .$.$.... !""""! +phiX174 1450 T 4 .$... """! +phiX174 1451 G 3 .$.. #"! +phiX174 1452 A 2 .$. "! +phiX174 1453 G 1 .$ ! |