| Next changeset 1:4b0418b1f58b (2021-11-09) |
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Commit message:
"planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101" |
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added:
instrain_profile.xml macros.xml test-data/N5_271_010G1.maxbin2.stb test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.IS.zip test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.IS.zip test-data/SmallScaffold.fa test-data/SmallScaffold.fa.sorted.bam |
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| diff -r 000000000000 -r 1f3730540302 instrain_profile.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/instrain_profile.xml Wed Aug 11 21:11:18 2021 +0000 |
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| b'@@ -0,0 +1,378 @@\n+<tool id="instrain_profile" name="InStrain Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Creates an inStrain profile (microdiversity analysis) from a mapping file </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="requirements">\n+ <requirement type="package" version="3.0">zip</requirement>\n+ </expand>\n+ <version_command>inStrain profile --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+#set ext=$mapping_input.datatype.file_ext\n+ln -s \'$mapping_input\' \'inputbam.$ext\'\n+#if $gene_profiling.gene_file\n+&&\n+ln -s \'$gene_profiling.gene_file\' \'gene_file.fna\'\n+#end if\n+#if $stb\n+&&\n+ln -s \'$stb\' \'stb_file.stb\'\n+#end if\n+&&\n+inStrain profile\n+ \'inputbam.$ext\'\n+ \'$sequence_input\'\n+ --output \'inStrain.IS\'\n+ $use_full_fasta_header\n+ --processes "\\${GALAXY_SLOTS:-6}"\n+ --min_mapq $read_filtering.min_mapq\n+ --max_insert_relative $read_filtering.max_insert_relative\n+ --min_insert $read_filtering.min_insert\n+ --pairing_filter \'$read_filtering.pairing_filter\'\n+#if $priority_reads\n+ --priority_reads \'$read_filtering.priority_reads\'\n+#end if\n+ $output.detailed_mapping_info\n+ --min_cov $variant_calling.min_cov\n+ --min_freq $variant_calling.min_freq\n+ --fdr $variant_calling.fdr\n+#if $gene_file\n+ --gene_file \'gene_file.fna\'\n+#end if\n+#if $stb\n+ --stb \'stb_file.stb\'\n+#end if \n+ $mm_level\n+#if $profile.database_mode\n+ $profile.database_mode\n+#else\n+ --min_read_ani $read_filtering.min_read_ani\n+ --min_genome_coverage $profile.min_genome_coverage\n+ $skip_mm_profiling\n+#end if\n+ --min_scaffold_reads $profile.min_scaffold_reads\n+ --min_snp $profile.min_snp\n+ $profile.store_everything\n+#if $profile.scaffolds_to_profile\n+ --scaffolds_to_profile \'$profile.scaffolds_to_profile\'\n+#end if\n+ --rarefied_coverage $profile.rarefied_coverage\n+ --window_length $profile.window_length\n+ $output.skip_genome_wide\n+ $output.skip_plot_generation\n+&&\n+cd ./inStrain.IS && zip -r ../inStrain.IS.zip *\n+ ]]></command>\n+ <inputs>\n+ <param name="mapping_input" type="data" format="bam,sam" label="A file containing metagenomic reads mapped to a DNA sequence" help="Sorted Bam file"/>\n+ <param name="sequence_input" type="data" format="fasta" label="A file containing a DNA sequence."/>\n+ <param argument="--use_full_fasta_header" type="boolean" truevalue="--use_full_fasta_header" falsevalue="" checked="false" label="Use full fasta header" help="Instead of using the fasta ID (space in header before space), use the full header. Needed for some mapping tools (including bbMap)"/>\n+ <section name="read_filtering" title="Read Filtering" expanded="true">\n+ <param argument="--min_read_ani" type="float" value="0.95" min="0" max="1" label="Minimum percent identity" help=" Minimum percent identity of read pairs to consensus to use the reads. Must be >, not >="/>\n+ <param argument="--min_mapq" type="integer" value="-1" label="Minimum mapq score" help="Minimum mapq score of EITHER read in a pair to use that pair. Must be >, not >="/>\n+ <param argument="--max_insert_relative" type="integer" value="3" label="Maximum insert relative" help="Multiplier to determine maximum insert size between two reads - default is to use 3x median insert size. Must be >, not >="/>\n+ <param argument="--min_insert" type="integer" value="50" label="Minimum insert" help="Minimum insert size between two reads - default is 50 bp. If two reads are 50bp each and overlap completely, their insert will be 50. Must be >, not >="/>\n+ <param argument="--pairing_filter" type="select" label="How should paired reads be handled?">\n+ <option value="paired_only" selected="true">Only paired reads are retained</option>\n+ <option value="non_'..b'r orientation with an expected insert size. The minimum insert distance can be set with the tool\'s corresponding parameter. The maximum insert distance is a multiple of the median insert distance. So if pairs have a median insert size of 500bp, by default all pairs with insert sizes over 1500bp will be excluded. For the max insert cutoff, the median_insert for all scaffolds is used.\n+ - Pairs must have a minimum mapQ score. MapQ scores are confusing and how they\xe2\x80\x99re calculated varies based on the mapping algorithm being used, but are meant to represent both the number of mismatches in the mapping and how unique that mapping is. With bowtie2, if the read maps equally well to two positions on the genome (multi-mapped read), its mapQ score will be set to 2. The read in the pair with the higher mapQ is used for the pair.\n+ - Pairs must be above some minimum nucleotide identity (ANI) value. For example if reads in a pair are 100bp each, and each read has a single mismatch, the ANI of that pair would be 0.99\n+\n+Next, using only read pairs that pass filters, a number of microdiversity metrics are calculated on a scaffold-by-scaffold basis. This includes:\n+\n+ - Calculate the coverage at each position along the scaffold\n+ - Calculate the nucleotide diversity at each position along the scaffold in which the coverage is greater than the min_cov argument.\n+ - Identify SNSs and SNVs. The criteria for being reported as a divergent site are 1) More than min_cov number of bases at that position, 2) More than min_freq percentage of reads that are a variant base, 3) The number of reads with the variant base is more than the null model for that coverage.\n+ - Calculate linkage between divergent sites on the same read pair. For each pair harboring a divergent site, calculate the linkage of that site with other divergent sites within that same pair. This is only done for pairs of divergent sites that are both on at least MIN_SNP reads\n+ - Calculate scaffold-level properties. These include things like the overall coverage, breadth of coverage, average nucleotide identity (ANI) between the reads and the reference genome, and the expected breadth of coverage based on that true coverage.\n+\n+Finally, this information is stored as an IS_profile object. This includes the locations of divergent sites, the number of read pairs that passed filters (and other information) for each scaffold, the linkage between SNV pairs, ect.\n+\n+Inputs\n+======\n+\n+A fasta file and a bam/sam file, \n+\n+Output\n+======\n+\n+An IS_profile. (Zip file), Containing:\n+ \n+1. scaffold_info.tsv\n+\n+ This gives basic information about the scaffolds in your sample at the highest allowed level of read identity.\n+\n+2. mapping_info.tsv\n+\n+ This provides an overview of the number of reads that map to each scaffold, and some basic metrics about their quality.\n+\n+3. SNVs.tsv\n+\n+ This describes the SNVs and SNSs that are detected in this mapping. While we should refer to these mutations as divergent sites, sometimes SNV is used to refer to both SNVs and SNSs.\n+\n+4. linkage.tsv\n+\n+ This describes the linkage between pairs of SNPs in the mapping that are found on the same read pair at least min_snp times.\n+\n+5. gene_info.tsv\n+\n+ This describes some basic information about the genes being profiled.\n+\n+6. genome_info.tsv\n+\n+ Describes many of the above metrics on a genome-by-genome level, rather than a scaffold-by-scaffold level. (To output it, set --skip_genome_wide to false)\n+\n+7. Figures/Plots (When --skip_plot_generation is set to false):\n+\n+ - Coverage and breadth vs. read mismatches\n+ - Genome-wide microdiversity metrics\n+ - Read-level ANI distribution\n+ - Major allele frequencies\n+ - Linkage decay\n+ - Read filtering plots\n+ - Scaffold inspection plot (large)\n+ - Linkage with SNP type (GENES REQUIRED)\n+ - Gene histograms (GENES REQUIRED)\n+\n+ ]]></help> \n+ <citations>\n+ <citation type="doi">10.1101/2020.01.22.915579</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 1f3730540302 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Aug 11 21:11:18 2021 +0000 |
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| @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.5.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0796</edam_topic> + <edam_topic>topic_3174</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0484</edam_operation> + <edam_operation>operation_3209</edam_operation> + <edam_operation>operation_3730</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">instrain</requirement> + <yield/> + </requirements> + </xml> + <token name="@HELP_HEADER@"> +What it does +============ + +inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification. + +Read more about the tool: https://instrain.readthedocs.io/en/latest/ + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2020.01.22.915579</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 1f3730540302 test-data/N5_271_010G1.maxbin2.stb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/N5_271_010G1.maxbin2.stb Wed Aug 11 21:11:18 2021 +0000 |
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| b'@@ -0,0 +1,167 @@\n+N5_271_010G1_scaffold_0 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_1 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_2 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_3 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_4 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_5 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_6 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_7 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_8 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_9 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_10 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_11 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_12 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_13 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_14 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_15 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_16 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_17 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_18 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_19 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_20 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_21 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_22 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_23 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_24 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_25 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_26 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_27 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_28 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_29 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_30 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_31 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_32 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_33 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_34 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_35 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_36 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_37 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_39 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_40 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_41 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_42 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_43 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_44 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_45 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_46 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_47 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_48 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_49 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_50 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_51 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_52 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_53 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_54 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_55 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_56 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_57 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_58 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_59 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_60 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_61 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_63 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_64 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_65 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_66 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_67 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_68 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_69 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_70 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_71 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_73 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_74 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_75 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_76 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_77 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_sc'..b'in2.maxbin.001.fasta\n+N5_271_010G1_scaffold_97 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_98 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_99 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_100 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_101 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_102 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_103 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_104 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_105 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_106 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_107 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_108 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_109 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_111 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_112 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_113 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_114 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_116 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_117 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_118 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_119 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_120 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_121 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_122 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_123 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_125 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_126 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_127 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_128 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_129 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_130 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_131 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_132 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_133 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_134 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_135 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_136 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_137 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_138 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_139 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_141 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_142 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_143 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_144 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_145 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_147 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_148 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_149 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_150 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_151 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_152 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_153 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_154 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_155 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_156 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_157 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_158 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_159 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_160 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_161 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_162 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_163 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_185 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_197 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_341 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_350 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_362 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_376 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_419 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_443 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_484 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_618 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_836 \t maxbin2.maxbin.001.fasta\n+N5_271_010G1_scaffold_963\tfobin.fasta\n' |
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| diff -r 000000000000 -r 1f3730540302 test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.IS.zip |
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| diff -r 000000000000 -r 1f3730540302 test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.IS.zip |
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| diff -r 000000000000 -r 1f3730540302 test-data/SmallScaffold.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SmallScaffold.fa Wed Aug 11 21:11:18 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>WeirdBoi +AAAAAAAAAAAAAAAAAAAAAAA +>N5_271_010G1_scaffold_963 read_length_150 read_count_3782 +TCTCCATTACATTCCATTCCATTCGGGTTGTTCCATTCCATTCCATTCCA +TTCCACTCCATTCCATTGCACTCGGGTTGATTCCATTCCATTCCATTCCG +GATGATTCCATTCCATTGCATTCCGT |
| b |
| diff -r 000000000000 -r 1f3730540302 test-data/SmallScaffold.fa.sorted.bam |
| b |
| Binary file test-data/SmallScaffold.fa.sorted.bam has changed |