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Use SAM headers from index directory's <prefix>.hdr if it exists #348

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Use SAM headers from index directory's <prefix>.hdr if it exists #348

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Commits on Mar 18, 2024

  1. Use SAM headers from index directory's <prefix>.hdr if present 

    Introduce a <prefix>.hdr file alongside the other index files, useful for
setting up detailed `@SQ` headers etc to be used by default when mapping.

Output SAM headers from: -H options; .hdr file stored with the index files;
the basic hard-coded `@HD`/`@SQ` default headers. An `@HD` header is always
printed, with -H overriding one from <prefix>.hdr (if any), which overrides
the default one. A set of `@SQ` headers is always printed, with -H options
overriding <prefix>.hdr overriding the default, similarly. Other headers
specified in either -H or <prefix>.hdr are all output.

If -H includes `@SQ` headers, we consider that the user has carefully
set up all headers to be output and ignore <prefix>.hdr entirely.

Add descriptions of <prefix>.alt (brief) and <prefix>.hdr (complete)
to the manual page. This <prefix>.hdr file is implemented for mem, bwase,
and bwape. It is not implemented for bwasw, which is deprecated.
    @jmarshall
    jmarshall committed Mar 18, 2024
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  2. Also accept SAM headers from <baseprefix>.dict if present 

    Now outputs SAM headers from: -H options; .hdr file stored with the
index files if present, or otherwise a .dict file if that is present;
the basic hard-coded `@HD`/`@SQ` default headers.
    @jmarshall
    jmarshall committed Mar 18, 2024
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