Add a footnote on case-insensitivity of RG PL (PR #684)

This is not changing what is valid / permitted, and indeed this
hopefully clarifies it further.  However the practicality of dealing
with wide-spread non-compliant data with lowercase PL values is that
tools may wish to be lenient and use case-insensitive matching.

Also removes test/sam/failed/hdr.RG6.sam due to explicitly testing
against the use of lower-case PL fields.  While strictly not
conforming, it's overly harsh if we are advocating a more
spec-tolerant testing regime for PL.

Fixes #679.

Author: jkbonfield

SAMv1.tex

@@ -329,7 +329,9 @@ \subsection{The header section}
   & {\tt PG} & Programs used for processing the read group.\\\cline{2-3}
   & {\tt PI} & Predicted median insert size, rounded to the nearest integer.\\\cline{2-3}
   & {\tt PL} & Platform/technology used to produce the reads. \emph{Valid values}:
-  {\tt CAPILLARY}, {\tt DNBSEQ} (MGI/BGI), {\tt ELEMENT}, {\tt HELICOS}, {\tt ILLUMINA}, {\tt IONTORRENT}, {\tt LS454}, {\tt ONT} (Oxford Nanopore), {\tt PACBIO} (Pacific Biosciences), {\tt SINGULAR}, {\tt SOLID}, and {\tt ULTIMA}.
+  {\tt CAPILLARY}, {\tt DNBSEQ} (MGI/BGI), {\tt ELEMENT}, {\tt HELICOS}, {\tt ILLUMINA}, {\tt IONTORRENT}, {\tt LS454}, {\tt ONT} (Oxford Nanopore), {\tt PACBIO} (Pacific Biosciences), {\tt SINGULAR}, {\tt SOLID}, and {\tt ULTIMA}.%
+\footnote{The {\tt PL} value should be written in uppercase exactly as shown in this list of valid values.
+Tools should also accept lowercase when reading the {\tt @RG PL} field, due to the existence of public data files with lowercase {\tt PL} values.}
   This field should be omitted when the technology is not in this list (though the {\tt PM} field may still be present in this case) or is unknown.\\\cline{2-3}
   & {\tt PM} & Platform model. Free-form text providing further details of the platform/technology used.\\\cline{2-3}
   & {\tt PU} & Platform unit (e.g., flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identifier.\\\cline{2-3}