Adding CRAM support

[muffato]

Fixes #54
Supersedes #176

The leg work was done by @s-andrews and @Pranav-Garg. All I've done here is an additional merge from master to make the PR clearer, and a few fixes regarding the JAR/classpath and the file extensions declared (and a couple of Java language fixes).

This fixes the bzip2 error I had flagged in #54 (comment). I've also tested all 162 CRAM files from the samtools test suite. The only failures are caused by:

• purposefully malformed CRAM files
• CRAM 3.1 and recent CRAM features (requires a newer version of htsjdk)

As far as I can see, upgrading htsjdk and supporting recent CRAM specs is as simple as putting a more recent htsjdk in, but the last version compatible with Java 11 is v3.0.5, from 3 years ago. Upgrading to the very latest htsjdk would mean bumping up the minimum Java version to 17. Don't know if that's something we can do, so I haven't committed that change.

[Copilot]

Pull request overview

This PR adds support for CRAM files as an input format to FastQC, addressing a long-standing feature request (#54). It routes .cram files through the existing BAMFile handler (which uses htsjdk), adds a --reference option to provide a FASTA reference file needed for CRAM decoding, and updates the classpath to include the commons-compress dependency required by the newer htsjdk for CRAM support. It also includes minor Java deprecation fixes in bundled Apache Commons Math source files.

Changes:

• CRAM file format detection, routing, and output filename handling added across SequenceFactory.java, SequenceFileFilter.java, FastQCConfig.java, OfflineRunner.java, and the fastqc Perl launcher script
• New --reference / -r option added to support providing a FASTA reference file for CRAM decoding in BAMFile.java, FastQCConfig.java, and the fastqc script
• Classpath updated in run_fastqc.bat, fastqc, and .classpath to include commons-compress-1.26.0.jar; and Java deprecation warnings fixed in bundled MathUtils.java and ResizableDoubleArray.java

Reviewed changes

Copilot reviewed 10 out of 11 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
uk/ac/babraham/FastQC/Sequence/SequenceFactory.java	Routes .cram extension and cram/cram_mapped format strings to BAMFile
uk/ac/babraham/FastQC/Sequence/BAMFile.java	Passes FASTA reference to SamReaderFactory when decoding CRAM files
uk/ac/babraham/FastQC/FileFilters/SequenceFileFilter.java	Adds .cram to the GUI file chooser filter
uk/ac/babraham/FastQC/FastQCConfig.java	Adds reference field and validates cram/cram_mapped format strings
uk/ac/babraham/FastQC/Analysis/OfflineRunner.java	Strips .cram extension when building the output HTML filename
fastqc	Adds --reference CLI option, updates classpath and help text for CRAM
run_fastqc.bat	Adds commons-compress-1.26.0.jar to the Windows classpath
.classpath	Adds Eclipse classpath entry for commons-compress-1.26.0.jar
org/apache/commons/math3/util/ResizableDoubleArray.java	Replaces deprecated new Float().hashCode() with Float.hashCode()
org/apache/commons/math3/util/MathUtils.java	Replaces deprecated new Double().hashCode() with Double.hashCode()

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