Add UMI support to samtools fastq / import. Needs htslib#1960#2270
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The bulk of these changes are in the associated htslib PR. This PR just adds CLI / usage information. Also fixed the generated header comment to remove trailing white space, and added missing CASAVA tag hints. Fix samtools fasta usage statement. Samtools fasta previously hid a lot of options from the usage statement despite them applying to both fasta and fastq outputs. Examples include setting compression level and use of various Casava tags. Some of these are unlikely combinations in FASTA output, but we now document all the options that affect output. Improved samtools fasta/fastq man page. Added the UMI options, but also added the undocumented -v option and updated the markup to be standard with italic (or underscored in nroff) for operands. Bug fixed the import SAM header comment to use -n instead of -N when documenting how to convert back to a single-ended fastq file. Fixes samtools#2259 Fixes samtools#2262
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The bulk of these changes are in the associated htslib PR. This PR just adds CLI / usage information.
Also fixed the generated header comment to remove trailing white space, and added missing CASAVA tag hints.
Fixes #2259
Fixes #2262
Draft as I forgot to update man pages. I'll do that tomorrow, but I wanted to get CI working (it failed due to CI flakiness before)