Developer options

Options useful mostly for developers of Genozip:

Usage: as flags for genozip (Z), genounzip (U), genocat (C), genols (L)

Note: When used with genocat most options show only the requested metadata and not the file data itself.

Memory consumption

--show-memory  ZUCL. Show what buffers are consuming the most memory.

kill -USR1 <pid>.  ZUCL. Executes --show-memory on a running process. Not available on Windows.

--debug-memory[=bytes]  ZUCL. Show Buffer allocations and destructions. If <bytes> is specified then show only allocations of at least <bytes>.

--show-hash  Z. See raw numbers that feed into determining the size of the global hash tables.

genozip file contents

--show-alleles  ZUC. (VCF only) Output allele values to stdout. Each row corresponds to a row in the VCF file. Mixed-ploidy regions are padded and 2-digit allele values are replaced by an ascii character.

--show-dict=field  ZUC. Show dictionaries read/written for each vblock. With optional <field> (eg CHROM ; RNAME ; POS ; AN etc) shows only that one field.

--show-b250=field  ZUC. Show b250 sections content - each value shows the line (counting from 1) and the index into its dictionary (note: REF and ALT are compressed together as they are correlated). With optional <field> (eg CHROM ; RNAME ; POS ; AN etc) shows only that one field. This also works with genounzip and genocat but without the line numbers.

--dump-b250=field.  ZUC.  Dump the binary content of the b250 data of this field exactly as they appear in the genozip format to a file named "<field>.b250" - specify the field name as it appears in the "Name" column in --SHOW-STATS for fields that have "comp b250" data.

--dump-local=field.  ZUC.  Same as --dump-b250 just for the "local" buffer.

--list-chroms.  ZUC.  List the names of the chromosomes (or contigs) included in the file.

--dump-section section-type.  ZUC. Dump the uncompressed unencrypted contents of all sections of this type (as it appears in --show-gheaders eg SEC_REFERENCE) to a files named "<section-type>.<vb>.<dict_id>.[header|body]".

--show-headers section-type.  ZUC. Show all the sections headers or those of a specific section type if the optional argument is provided. Argument is a case-insesitive substring of a section name.

--show-index  ZUC. Show the content of the random access index (SEC_RANDOM_ACCESS section).

--show-reference  ZUC. Show the ranges included the SEC_REFERENCE sections.

--show-ref-seq  ZUC. Show the reference sequences as stored in genozip file or a reference file. Combine with --regions to see specific regions (genocat only). Combine with --sequential to omit newlines. '-' appears in unset loci. Note: the sequence stored in a .ref.genozip is NOT 100% identical to the FASTA that was used to generate it.

--show-ref-index  ZUC. Show the content of the random access index of the reference data (SEC_REF_RAND_ACC section).

--show-ref-hash  ZUC. Show the details of the reference hash table (SEC_REF_HASH) sections.

--show-ref-contigs  ZUC. Show the details of the reference contigs.

--show-ref-alts  ZUC. Show the details of the file contigs that are mapped to a different contig name in the reference (eg '22' -> 'chr22').

--show-txt-contigs  ZUC. (SAM and BAM) Show the details of the contigs appearing the file header (SQ lines).

--show-gheader  ZUC.  Show the content of the genozip header (which also includes the list of all sections in the file).

--show-vblocks  ZUC.  Show vblock headers as they are read / written.

--show-aliases  ZUC. See contents of SEC_DICT_ID_ALIASES section.

--show-reference  ZUC. Show the ranges included the SEC_REFERENCE sections.

--show-is-set contig.  UC. Shows the contents of SEC_REF_IS_SET section for the given contig.

--show-bgzf  ZUC. Show BGZF blocks as they are being compressed or decompressed.

Tracking execution

--show-containers  ZUC. Show flow of containers.

--show-threads  ZUC.  Show thread dispatcher activity.

--debug-progress  ZUC. See raw numbers that feed into the progress indicator.

--show-time=res. ZUCL. Show what functions are consuming the most time. Optional <res> is one of the members of ProfilerRec defined in profiler.h such 'compressor_lzma' or a substring such as 'compressor_'.

--show-digest  ZUC. Show digest (MD5 or Adler32) updates.

--show-mutex[=mutex-name].  ZUC. Shows locks and unlocks of all mutexes or a particular mutex.

Tracking compression performance

-w, --show-stats   Show the internal structure of a genozip file and the associated compression statistics.

-W, --SHOW-STATS   Show more detailed statistics.

--show-codec  Z. Genozip tests for the best codec when it first encounters a new type of data. See the results.

Controlling execution

--one-vb vb  C. Reconstruct data from a single VB

--seg-only  Z. Run the segmenter but don't compress and don't write the output

--xthreads  ZUC. Use only one thread for the main PIZ/ZIP dispatcher. This doesn't affect thread use of other dispatchers,