- rewritten for greater experimental flexibility
- the AA peak can be included in the fit (the -i option)
- the minimum fraction of aberrant cells as a command line parameter (-m)
- control the minimum cn4 bump size (-b)

…r CN4

…lute; hidden --force-cn option for debugging

This was hidden as it was/is experimental, but with the licensing
additions, users are explicitly requesting the command by compiling
with USE_GPL=1, so we might as well display in the help message.

Closes samtools#280

updates to polysomy command for publication

Resolves samtools#248

…g in -e -

updates to roh command for publication

…ings: <snps|indels|both|all|none>

bcf_hdr_combine deprecated and replaced by bcf_hdr_merge in htslib
(2bb9370f5a24938d8a2dc56f404e584661bf413f).

Fixes samtools#208

… well)

…erying FMT vectors, such as PL{0}

- CNx state removed
- automatic optimization of parameters to increase sensitivity when
only a fraction of cells is aberrant (at the cose of decreased specificity)
- LRR smoothing

…mean

See also 1f81d25 and samtools/htslib@3fcf7c9

Fixes samtools#285

Petentially fixes samtools#284

…m a VCF

Closes samtools#294

…ferences in FMT/AD

* add tests for samtools#452 and samtools#439

Resolves samtools#452

Not functional yet. Just copying over the files.

* bam_plcmd.c for the mpileup command
* bam2bcf.[ch] bam2bcf_indel.c for the VCF/BCF creation
* sample.[ch] for RG:SM handling

minimal changes to files copied from samtools in order to compile
in bcftools.

* use regidx from htslib rather than bedidx from samtools
* remove sam_opts calls as sam_opts.h not copied from samtools

Todo:

* copy over relevant functionality from sam_opts.h
* remove text based mpileup output
* update options and defaults
* bring over `---gvcf` and other changes from @pd3 fork

* deprecate `-g -v -u` options (still functional, but with warning)
* exit with message to use `samtools mpileup` if `-s/--output-MQ` used
* `-O` option was `--output-BP` and is not `--output-type` for consistency
  with other bcftools commands. If `[buzv]` not given as an option
  will warn

These catches for old text output options are probably not necessary
as users may not expect text output from `bcftools mpileup`.

* mpileup.1.out, mpileup.2.out, mpileup.3.out and mpileup.4.out
  are from samtools with mpileup.1.out and mpileup.3.out converted
  from the text output
* mpileup.5.out a new test with the newer AD, etc annotations
* sam/bam/cram test files all stored. perhaps there is some
  way to store one version and convert within the test ala
  the vcf-miniview in samtools?

adds to @4e7c8fb86349761fed1b290357dbc792222ecdcb

* remove deprecated `-g`, `-v`, `-u`, `-D`, `-V`, `-S`
* remove `-R` short option to make way for `--regions-file` option later

This commit brings over the `--gvcf` functionality from @pd3's branch,
consisting of relevant bits from cf3219c
and ee8210d

Reference only blocks will be merged into gVCF blocks when the
minimum per-sample depth falls in the intervals defined by the
argument to the `-gvcf` option. Documentaion added to explain
the merging and a test added.

pulling over of cf5c354
adding in `-S,--samples-file` option and exiting if no samples are
read from the file or list

TODO: add exclude logic with `^` prefix as in other bcftools commands

removed `config.h` from `sample.c` as leftover this is in samtools,
but not bcftools at the moment

switch `-t/--output-tags` option to `-a/--annotate` to make room for
the `-t/--targets` option

available annotations are now listed on request with `-a ?` rather than
cluttering up the help output.

This is meant as a temporary change while we extend the
regidx api, but allow bcftools code to use these changes
before they appear in some form in htslib.

This commit does not add new features, just copies over
`regidx.[ch]` and rejiggers the linking to use these
local bcftools copies.

the `*_c` are removed due to relying on `hts_internal.h`
(see fc9aeb6f77668afed412119701c5c58b0fca8091)

* added functions to loop over all regions
* lazy index build in case random access is not required
* support for chromosome names only, beg-end coordinates not mandatory
* set cap at maximum coordinate at 2147483647, hts_itr does not support larger
* tab and reg parsers will throw on finding a `0` to catch user
  error of using 0-based rather than 1-based coords

* `-r/--region` replaced by `-r/--regions` which will accept a comma separated
  list of regions as in other bcftools commands. `--region` still accepted
* `-R/--regions-file` option added to read regions from a file

This commit lifts over work originally done in cfd7cf9

Note: when more than one region is given, all indices are stored in memory,
which can be a problem when running on many bams. An alternative would be
to cache pre-filled `hts_itr`'s for each region.

Resolves samtools#369

see samtools/samtools@91283dd

…ools commands

the point of `--no-version` is to remove invocation specify metadata in the header
lines for pipeline systems that are tracking this separately. we are outputting
the `##reference` line though in mpileup. could drop this as well when
`--no-version` used. seems silly to add a separate option.

* prefix with ^ to negate the selection
* assign/rename samples by providing second field:
    RG_ID_1  SAMPLE_A
    RG_ID_2  SAMPLE_A
    RG_ID_3  SAMPLE_B
* on read group name conflict give the alignment file,
  asterisk for all reads in the file:
    RG_ID_1  FILE_1.bam  SAMPLE_A
    RG_ID_2  FILE_2.bam  SAMPLE_A
    *        FILE_3.bam  SAMPLE_C

Resolves 4th item in
samtools#414 (comment)
and samtools/samtools#324.

Our first foray into exploiting this is to cache the
bam_smpl_get_sample_id return value.  We compute this once in the
constructor (the first time we see a new bam1_t) instead of for every
pileup location in group_smpl.

TO DO: Group_smpl itself could now become distributed perhaps.  Rather
than an N*M loop clustering all sample IDs together, each new bam
could be added to sample struct on first appearance and removed when
it goes out of sight.

The slight caveat preventing this from being implemented immediately
is that the constructor/destructors are called for every BAM
overlapping the region rather than every filtered base that ultimately
ends up in a pileup.  Indeed sometimes we get constructors for
reads entirely filtered out.

Mann Whitney test now uses a precomputed table instead of continually
calculating the same values many times over.

calc_mwu_bias now has short-cuts to compute the result faster when one
or both of a[] and b[] hold zero values.