Fix hts_hfile() for compressed text_format files #1826
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SAM and VCF files opened for write both start with htsFile::format.format set to text_format, and then update it after writing the header. This means it's possible to open a text_format file with compression, so hts_hfile() needs to handle it in the same way as sam and vcf. Noticed when hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE) failed in samtools sort in the case where fpout was a compressed sam file. At this point fpout was a text_file, so the wrong pointer was passed to hfile_set_blksize(), which luckily bailed out and returned -1 before doing any damage to the incorrectly passed-in structure.
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SAM and VCF files opened for write both start with
htsFile::format.formatset totext_format, and then update it after writing the header. This means it's possible to open atext_formatfile with compression, sohts_hfile()needs to handle it in the same way as SAM and VCF.Noticed when
hts_set_opt(fpout, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE)failed insamtools sortin the case where the output was a compressed SAM file. At this pointfpoutwas atext_file, so the wrong pointer was passed tohfile_set_blksize(), which luckily bailed out and returned -1 before doing any damage to the incorrectly passed-in structure.