7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

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-.TH tabix 1 "15 December 2015" "htslib-1.3" "Bioinformatics tools"
-.SH NAME
-.PP
-bgzip \- Block compression/decompression utility
-.PP
-tabix \- Generic indexer for TAB-delimited genome position files
-.\"
-.\" Copyright (C) 2009-2011 Broad Institute.
-.\"
-.\" Author: Heng Li <lh3@sanger.ac.uk>
-.\"
-.\" Permission is hereby granted, free of charge, to any person obtaining a
-.\" copy of this software and associated documentation files (the "Software"),
-.\" to deal in the Software without restriction, including without limitation
-.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
-.\" and/or sell copies of the Software, and to permit persons to whom the
-.\" Software is furnished to do so, subject to the following conditions:
-.\"
-.\" The above copyright notice and this permission notice shall be included in
-.\" all copies or substantial portions of the Software.
-.\"
-.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-.\" DEALINGS IN THE SOFTWARE.
-.\"
-.SH SYNOPSIS
-.PP
-.B bgzip
-.RB [ -cdhB ]
-.RB [ -b
-.IR virtualOffset ]
-.RB [ -s
-.IR size ]
-.RI [ file ]
-.PP
-.B tabix
-.RB [ -0lf ]
-.RB [ -p
-gff|bed|sam|vcf]
-.RB [ -s
-.IR seqCol ]
-.RB [ -b
-.IR begCol ]
-.RB [ -e
-.IR endCol ]
-.RB [ -S
-.IR lineSkip ]
-.RB [ -c
-.IR metaChar ]
-.I in.tab.bgz
-.RI [ "region1 " [ "region2 " [ ... "]]]"
-
-.SH DESCRIPTION
-.PP
-Tabix indexes a TAB-delimited genome position file
-.I in.tab.bgz
-and creates an index file (
-.I in.tab.bgz.tbi
-or 
-.I in.tab.bgz.csi
-) when
-.I region
-is absent from the command-line. The input data file must be position
-sorted and compressed by
-.B bgzip
-which has a
-.BR gzip (1)
-like interface. After indexing, tabix is able to quickly retrieve data
-lines overlapping
-.I regions
-specified in the format "chr:beginPos-endPos". Fast data retrieval also
-works over network if URI is given as a file name and in this case the
-index file will be downloaded if it is not present locally.
-
-.SH INDEXING OPTIONS
-.TP 10
-.B -0, --zero-based
-Specify that the position in the data file is 0-based (e.g. UCSC files)
-rather than 1-based.
-.TP
-.BI "-b, --begin " INT
-Column of start chromosomal position. [4]
-.TP
-.BI "-c, --comment " CHAR
-Skip lines started with character CHAR. [#]
-.TP
-.BI "-C, --csi"
-Skip lines started with character CHAR. [#]
-.TP
-.BI "-e, --end " INT
-Column of end chromosomal position. The end column can be the same as the
-start column. [5]
-.TP
-.B "-f, --force "
-Force to overwrite the index file if it is present.
-.TP
-.BI "-m, --min-shift" INT
-set minimal interval size for CSI indices to 2^INT [14]
-.TP
-.BI "-p, --preset " STR
-Input format for indexing. Valid values are: gff, bed, sam, vcf.
-This option should not be applied together with any of
-.BR -s ", " -b ", " -e ", " -c " and " -0 ;
-it is not used for data retrieval because this setting is stored in
-the index file. [gff]
-.TP
-.BI "-s, --sequence " INT
-Column of sequence name. Option
-.BR -s ", " -b ", " -e ", " -S ", " -c " and " -0
-are all stored in the index file and thus not used in data retrieval. [1]
-.TP
-.BI "-S, --skip-lines " INT
-Skip first INT lines in the data file. [0]
-
-.SH QUERYING AND OTHER OPTIONS
-.TP
-.B "-h, --print-header "
-Print also the header/meta lines.
-.TP
-.B "-H, --only-header "
-Print only the header/meta lines.
-.TP
-.B "-l, --list-chroms "
-List the sequence names stored in the index file.
-.TP
-.B "-r, --reheader " FILE
-Replace the header with the content of FILE
-.TP
-.B "-R, --regions " FILE
-Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz 
-file name extension) or a TAB-delimited file with CHROM, POS, and,  optionally,
-POS_TO columns, where positions are 1-based and inclusive.  When this option is in use, the input
-file may not be sorted. 
-regions.
-.TP
-.B "-T, --targets" FILE
-Similar to 
-.B -R
-but the entire input will be read sequentially and regions not listed in FILE will be skipped.
-.PP
-.SH EXAMPLE
-(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
-
-tabix -p gff sorted.gff.gz;
-
-tabix sorted.gff.gz chr1:10,000,000-20,000,000;
-
-.SH NOTES
-It is straightforward to achieve overlap queries using the standard
-B-tree index (with or without binning) implemented in all SQL databases,
-or the R-tree index in PostgreSQL and Oracle. But there are still many
-reasons to use tabix. Firstly, tabix directly works with a lot of widely
-used TAB-delimited formats such as GFF/GTF and BED. We do not need to
-design database schema or specialized binary formats. Data do not need
-to be duplicated in different formats, either. Secondly, tabix works on
-compressed data files while most SQL databases do not. The GenCode
-annotation GTF can be compressed down to 4%.  Thirdly, tabix is
-fast. The same indexing algorithm is known to work efficiently for an
-alignment with a few billion short reads. SQL databases probably cannot
-easily handle data at this scale. Last but not the least, tabix supports
-remote data retrieval. One can put the data file and the index at an FTP
-or HTTP server, and other users or even web services will be able to get
-a slice without downloading the entire file.
-
-.SH AUTHOR
-.PP
-Tabix was written by Heng Li. The BGZF library was originally
-implemented by Bob Handsaker and modified by Heng Li for remote file
-access and in-memory caching.
-
-.SH SEE ALSO
-.PP
-.BR samtools (1)