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@@ -52,23 +52,23 @@
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////////////////////////////////////////////////////////////////////
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BamToEgg::
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BamToEgg() :
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- SomethingToEgg("Bam", ".bam")
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+ SomethingToEgg("bam", ".bam")
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{
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add_path_replace_options();
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add_path_store_options();
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set_program_description
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- ("This program converts native Panda Bam files to egg. The conversion "
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+ ("This program converts native Panda bam files to egg. The conversion "
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"is somewhat incomplete; running egg2bam followed by bam2egg should not "
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- " be expected to yield the same egg file you started with.");
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+ "be expected to yield the same egg file you started with.");
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redescribe_option
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("cs",
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"Specify the coordinate system of the input " + _format_name +
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- " file. By default, this is taken from the Configrc file, which "
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- "is currently " + format_string(default_coordinate_system) + ".");
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+ " file. By default, this is taken from the Config.prc file, which "
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+ "is currently " + format_string(get_default_coordinate_system()) + ".");
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- _coordinate_system = default_coordinate_system;
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+ _coordinate_system = get_default_coordinate_system();
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}
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////////////////////////////////////////////////////////////////////
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