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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.19">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
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7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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8 <action type="shell_command">make</action>
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9 <action type="move_file">
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10 <source>samtools</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>
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19 Program: samtools (Tools for alignments in the SAM format)
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20 Version: 0.1.19
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21
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22 Usage: samtools <command> [options]
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23
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24 Command: view SAM<->BAM conversion
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25 sort sort alignment file
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26 mpileup multi-way pileup
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27 depth compute the depth
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28 faidx index/extract FASTA
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29 tview text alignment viewer
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30 index index alignment
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31 idxstats BAM index stats (r595 or later)
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32 fixmate fix mate information
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33 flagstat simple stats
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34 calmd recalculate MD/NM tags and '=' bases
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35 merge merge sorted alignments
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36 rmdup remove PCR duplicates
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37 reheader replace BAM header
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38 cat concatenate BAMs
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39 targetcut cut fosmid regions (for fosmid pool only)
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40 phase phase heterozygotes
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41 </readme>
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42 </package>
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43 </tool_dependency>
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