Miscellaneous minor build infrastructure and code fixes #1807
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These files can appear in base_mods, fastq, mpileup, and sam_filter as well as faidx and tabix.
As noted in samtools#1722, this function was removed in PR samtools#1672.
Plain getopt() is declared in <unistd.h>; strcasecmp() et al are only portably declared in <strings.h>.
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All look good to me. Squashed and merge as suggested. |
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Accumulated extremely squashable minor build infrastructure and code fixes:
Ignore and clean
test/*/FAIL*for six subdirectories — these files can appear in base_mods, fastq, mpileup, and sam_filter as well as faidx and tabix.Fix MM-explicit.sam comment header to use
@CO\tas per other comment headers.Remove extraneous inclusion and add missing dependency.
Remove last traces of previously deleted
bgzf_idx_amend_last()— as noted in formerly caught bgzf_idx_amend_last symbol #1722, this function was removed in PR Fix multi-threaded on-the-fly indexing problems #1672.Use
isspace_c()et al in annot-tsv.c.