Add opt-in planned parser for VCF FORMAT fields

.gitignore

@@ -65,6 +65,7 @@ shlib-exports-*.txt
 /test/test_bgzf
 /test/test_expr
 /test/test_faidx
+/test/test_format_plan_cache
 /test/test_index
 /test/test_introspection
 /test/test_kfunc

Makefile

@@ -94,6 +94,7 @@ BUILT_TEST_PROGRAMS = \
 	test/test_str2int \
 	test/test_time_funcs \
 	test/test_view \
+	test/test_format_plan_cache \
 	test/test_index \
 	test/test-vcf-api \
 	test/test-vcf-sweep \
@@ -690,6 +691,7 @@ check test: all $(HTSCODECS_TEST_TARGETS)
 	test/test_str2int
 	test/test_time_funcs
 	test/fieldarith test/fieldarith.sam
+	test/test_format_plan_cache
 	test/hfile
 	if test "x$(BUILT_PLUGINS)" != "x"; then \
 	    HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR); \
@@ -790,6 +792,9 @@ test/test_time_funcs: test/test_time_funcs.o
 test/test_view: test/test_view.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread
 
+test/test_format_plan_cache: test/test_format_plan_cache.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_format_plan_cache.o libhts.a $(LIBS) -lpthread
+
 test/test_index: test/test_index.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test_index.o libhts.a $(LIBS) -lpthread
 
@@ -885,6 +890,7 @@ test/test-regidx.o: test/test-regidx.c config.h $(htslib_kstring_h) $(htslib_reg
 test/test_str2int.o: test/test_str2int.c config.h $(textutils_internal_h)
 test/test_time_funcs.o: test/test_time_funcs.c config.h $(hts_time_funcs_h)
 test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_hts_log_h)
+test/test_format_plan_cache.o: test/test_format_plan_cache.c config.h $(htslib_kstring_h) $(htslib_vcf_h)
 test/test_faidx.o: test/test_faidx.c config.h $(htslib_faidx_h)
 test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h)
 test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(htslib_kstring_h) $(htslib_kseq_h)

docs/FORMAT_PLAN_OVERVIEW.md

@@ -0,0 +1,147 @@
+# VCF FORMAT Planner Review Notes
+
+This is an interim review note for the opt-in VCF FORMAT planner in `vcf.c`.
+It is intended to make the implementation easier to review in this branch; it
+is not proposed as permanent user-facing documentation.
+
+## Purpose
+
+The planner is an optional fast path for parsing VCF sample `FORMAT` columns
+into BCF.  It is disabled by default and only runs when:
+
+```sh
+HTS_VCF_FORMAT_PLAN=1
+```
+
+Unset, `0`, or unknown values use the existing generic parser.  The hard
+correctness rule is byte-identical BCF output compared with the generic parser.
+Any unsupported or suspicious FORMAT column falls back for the whole column.
+
+`HTS_VCF_FORMAT_PLAN_STATS=1` enables temporary diagnostic counters for review
+and benchmarking.  These environment variables are branch controls, not stable
+public API.
+
+## Entry Point
+
+`vcf_parse_format()` tries `vcf_parse_format_planned()` before the generic
+FORMAT parser when the environment gate is enabled.  The planned parser returns
+success only after it has fully emitted the FORMAT column.  It returns the
+fallback code before the caller invokes the generic parser when compilation,
+width resolution, parsing, or row validation does not meet the supported
+contract.
+
+The planned path never commits partial FORMAT output after detecting a row-local
+failure.  Rollback and fallback are part of the normal control flow.
+
+## Plan Cache
+
+Plans are stored in private `bcf_hdr_aux_t` state.  Cache keys are the literal
+FORMAT string plus the active private header generation.  The cache stores both
+supported and unsupported plans so repeated unsupported schemas avoid repeated
+tokenization and metadata lookup.
+
+`bcf_hdr_sync()` clears cached plans and advances the generation because FORMAT
+ids, types, and lengths are header-local.  The planner refuses dirty headers.
+
+## Compilation
+
+Compilation works from header metadata rather than exact whole-FORMAT string
+kernels.  For each FORMAT token, the compiler records:
+
+- the header id;
+- declared type;
+- declared number model;
+- whether the row needs record-local width resolution or sample-text scanning;
+- the executor row kind.
+
+The compiler rejects empty tokens, undefined tags, duplicate tags, unsupported
+types or number models, and non-standard `GT` declarations.  Tokenization does
+not collapse empty fields, so malformed schemas such as `GT::DP` still fall
+back in a way that preserves generic-parser behavior.
+
+## Supported Rows
+
+The current executor has six row kinds:
+
+- `GT2`
+- `INT1`
+- `INTVEC`
+- `FLOAT1`
+- `FLOATN`
+- `STR`
+
+The earlier width-specific integer-vector row kinds were removed.  A single
+`INTVEC` path handles fixed and row-local integer widths, including the
+over-width comma check needed to preserve fallback behavior.
+
+Supported shapes include:
+
+- simple diploid `GT` values with one-character alleles or missing values,
+  separated by `/` or `|`, including phased-missing forms such as `.|.`,
+  `0|.`, and `.|0`;
+- integer and float scalar fields;
+- integer and float vector fields within the planner width cap;
+- numeric `Number=A`, `Number=R`, and `Number=G` widths resolved from the
+  current record allele count;
+- bounded measured `Number=.` numeric rows;
+- bounded `Type=String,Number=1` rows;
+- selected-sample parsing via `bcf_hdr_set_samples()`.
+
+Unsupported or intentionally generic cases include undefined tags, duplicate
+FORMAT tags, dirty headers, unsupported type or number declarations, unsupported
+GT encodings, malformed separators, unsafe row widths, and string/float-heavy
+layouts that do not benefit from planning.
+
+## Width Resolution
+
+Header-fixed rows use the declared width directly, after resolving
+allele-dependent widths for the current record.  Numeric widths must fit the
+planner cap of 64 values.
+
+Measured numeric and string rows perform a first pass over original sample
+columns.  This is required to match the generic parser's width and padding
+rules.  If samples are selected, the planner still scans original sample
+columns but measures and emits retained samples densely.
+
+Strings are capped at 256 bytes in the planned path.  Wider string rows fall
+back for the whole FORMAT column.
+
+## Fallback Contract
+
+Fallback is expected and intentional.  It happens before generic parsing when
+the compiler or row executor sees unsupported structure, unsupported widths,
+unexpected separators, unsupported GT shape, parse failures, sample-count
+mismatch, or allocation/internal consistency errors.
+
+Diagnostic fallback reasons are:
+
+- `unsupported`
+- `numeric_width`
+- `string_width`
+- `gt_shape`
+- `parse`
+- `separator`
+- `sample_count`
+
+## Test And Benchmark Evidence
+
+Focused correctness checks used for this review branch:
+
+```sh
+make test/test_view test/test_format_plan_cache bgzip tabix
+./test/test_format_plan_cache
+perl test/test.pl -F test_vcf_format_plan
+test/maintainer/check_spaces.pl vcf.c docs/FORMAT_PLAN_OVERVIEW.md \
+  test/format-plan-malformed-fields.vcf test/test.pl
+git diff --check
+```
+
+The focused FORMAT-plan test fragment covers disabled/unknown environment
+behavior, selected samples, malformed FORMAT tokens, malformed numeric fields,
+phased missing GT values, cache invalidation after header metadata changes, and
+fallback after partial planned parsing.
+
+The current public-fork PR body contains the maintainer-facing performance
+summary.  The compact benchmark artifacts live on the corpus branch
+`feature/vcf-parsing-speedup-corpus`, including the current `test_view` and
+bcftools summaries for commit `bd643182c8fa722abbc0cb89860263a90bb97020`.

test/format-plan-cache.vcf

@@ -0,0 +1,61 @@
+##fileformat=VCFv4.3
+##contig=<ID=1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=F01,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F02,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F03,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F04,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F05,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F06,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F07,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F08,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F09,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F10,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F11,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F12,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F13,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F14,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F15,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F16,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F17,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F18,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F19,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=F20,Number=1,Type=Integer,Description="Cache test field">
+##FORMAT=<ID=LONGFORMATFIELD01,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD02,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD03,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD04,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD05,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD06,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD07,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD08,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD09,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD10,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD11,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD12,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD13,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD14,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD15,Number=1,Type=Integer,Description="Long cache test field">
+##FORMAT=<ID=LONGFORMATFIELD16,Number=1,Type=Integer,Description="Long cache test field">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2
+1	1	.	A	C	.	PASS	.	GT:F01	0/1:1	1/1:2
+1	2	.	A	C	.	PASS	.	GT:F02	0/1:2	1/1:3
+1	3	.	A	C	.	PASS	.	GT:F03	0/1:3	1/1:4
+1	4	.	A	C	.	PASS	.	GT:F04	0/1:4	1/1:5
+1	5	.	A	C	.	PASS	.	GT:F05	0/1:5	1/1:6
+1	6	.	A	C	.	PASS	.	GT:F06	0/1:6	1/1:7
+1	7	.	A	C	.	PASS	.	GT:F07	0/1:7	1/1:8
+1	8	.	A	C	.	PASS	.	GT:F08	0/1:8	1/1:9
+1	9	.	A	C	.	PASS	.	GT:F09	0/1:9	1/1:10
+1	10	.	A	C	.	PASS	.	GT:F10	0/1:10	1/1:11
+1	11	.	A	C	.	PASS	.	GT:F11	0/1:11	1/1:12
+1	12	.	A	C	.	PASS	.	GT:F12	0/1:12	1/1:13
+1	13	.	A	C	.	PASS	.	GT:F13	0/1:13	1/1:14
+1	14	.	A	C	.	PASS	.	GT:F14	0/1:14	1/1:15
+1	15	.	A	C	.	PASS	.	GT:F15	0/1:15	1/1:16
+1	16	.	A	C	.	PASS	.	GT:F16	0/1:16	1/1:17
+1	17	.	A	C	.	PASS	.	GT:F17	0/1:17	1/1:18
+1	18	.	A	C	.	PASS	.	GT:F18	0/1:18	1/1:19
+1	19	.	A	C	.	PASS	.	GT:F19	0/1:19	1/1:20
+1	20	.	A	C	.	PASS	.	GT:F20	0/1:20	1/1:21
+1	21	.	A	C	.	PASS	.	GT:LONGFORMATFIELD01:LONGFORMATFIELD02:LONGFORMATFIELD03:LONGFORMATFIELD04:LONGFORMATFIELD05:LONGFORMATFIELD06:LONGFORMATFIELD07:LONGFORMATFIELD08:LONGFORMATFIELD09:LONGFORMATFIELD10:LONGFORMATFIELD11:LONGFORMATFIELD12:LONGFORMATFIELD13:LONGFORMATFIELD14:LONGFORMATFIELD15:LONGFORMATFIELD16	0/1:1:2:3:4:5:6:7:8:9:10:11:12:13:14:15:16	1/1:2:3:4:5:6:7:8:9:10:11:12:13:14:15:16:17

test/format-plan-composable.vcf

@@ -0,0 +1,16 @@
+##fileformat=VCFv4.3
+##contig=<ID=chr22,length=50818468>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods">
+##FORMAT=<ID=XX,Number=2,Type=Integer,Description="Fixed-width extension values">
+##FORMAT=<ID=XS,Number=1,Type=String,Description="String extension value">
+##FORMAT=<ID=VX,Number=.,Type=Integer,Description="Variable-width fallback values">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
+chr22	10610000	.	A	T	50	PASS	.	GT:AD	0/1:4,5	0/0:9,0	./.:0,0
+chr22	10610010	.	A	T	50	PASS	.	GT:AD:DP:XX:PL	0/1:4,5:9:7,8:90,0,120	0/0:9,0:9:1,2:0,30,200	./.:0,0:0:.,.:.
+chr22	10610020	.	A	C,G	50	PASS	.	DP:XS:GT:XX:AD:GQ:PL	12:alpha:1/2:3,4:1,5,6:60:100,90,80,70,0,20	8:beta:0/2:5,6:4,0,4:35:80,70,60,50,40,0	0:.:./.:.,.:0,0,0:.:.
+chr22	10610030	.	G	C	50	PASS	.	GT:AD:DP:GQ:PL	0/1:3,4:7:50:70,0	0/0:6,0:6:35:0,50	./.:0,0:0:.:.
+chr22	10610040	.	G	C	50	PASS	.	GT:AD:DP:VX:PL	0/1:3,4:7:1,2,3:70,0,90	0/0:6,0:6:5:0,50,120	./.:0,0:0:.:.

test/format-plan-edge.vcf

@@ -0,0 +1,38 @@
+##fileformat=VCFv4.3
+##contig=<ID=chr22,length=50818468>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype quality">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Filter">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype likelihoods">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Strand bias table">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
+chr22	10510061	.	A	T	64.12	PASS	.	GT:AB:AD:DP:GQ:PL	0/0:.:3,0:3:9:0,9,104	0/1:0.5:5,4:9:99:99,0,123	./.:.:0,0:0:.:.
+chr22	10510352	.	AT	A	50	PASS	.	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:10510352_AT_A:225,15,0	0/1:3,2:5:20:0|1:10510352_AT_A:20,0,200	./.:0,0:0:.:.:.:.
+chr22	10520000	.	A	C,G	50	PASS	.	GT:AD:DP:GQ:PL	1/2:1,4,5:10:60:100,80,70,60,0,20	0/2:3,0,2:5:30:80,70,60,50,40,0	./.:0,0,0:0:.:.
+chr22	10530000	.	G	A	50	PASS	.	GT:DP:AD:GQ:PL	0/1:7:3,4:42:99,0,120	0/0:5:5,0:15:0,15,200	./.:0:0,0:.:.
+chr22	10540000	.	C	T	50	PASS	.	GT:HQ:DP:GQ	0/1:10,20:7:40	0/0:.,.:5:50	./.:.:0:.
+chr22	10550000	.	C	T	50	PASS	.	GT:FT:DP:GQ	0/1:PASS:7:40	0/0:LowQual:5:50	./.:.:0:.
+chr22	10560000	.	A	C,G	50	PASS	.	GT:GL:DP:GQ	0/1:-0.1,-1.2,-9.9,-2.0,-3.0,-4.0:7:40	1/2:-9.9,-8.8,-7.7,-6.6,-5.5,-4.4:5:50	./.:.:0:.
+chr22	10570000	.	A	T	50	PASS	.	GT:AD:DP:GQ:PL	0:3,0:3:10:0,10,100	1:0,3:3:20:100,10,0	.:0,0:0:.:.
+chr22	10580000	.	A	C,G,T,AA,AC,AG,AT,CA,CC,CG	50	PASS	.	GT:AD:DP:GQ:PL	10/10:0,0,0,0,0,0,0,0,0,0,7:7:20:200,190,180,170,160,150,140,130,120,110,100,90,80,70,60,50,40,30,20,10,0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460	0/10:3,0,0,0,0,0,0,0,0,0,2:5:30:0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250,260,270,280,290,300,310,320,330,340,350,360,370,380,390,400,410,420,430,440,450,460,470,480,490,500,510,520,530,540,550,560,570,580,590,600,610,620,630,640,650	./.:0,0,0,0,0,0,0,0,0,0,0:0:.:.
+chr22	10585000	.	A	T	50	PASS	.	GT:AD:DP:GQ:PL	0/0:.:3:10:.	0/1:.:5:20:.	./.:.:0:.:.
+chr22	10586000	.	A	T	50	PASS	.	GT:AD:DP:GQ:PL	0/1:3,4:7:50:90,0,120	0/1:3:3:20:80,0	./.:0,0:0:.:.
+chr22	10587000	.	A	C,G	50	PASS	.	GT:AD:DP:GQ:PL	1/2:1,4,5:10:60:100,80,70,60,0,20	0/2:.:5:30:.	./.:0,0,0:0:.:.
+chr22	10590000	.	A	T	50	PASS	.	DP:GQ:GT:AD:PL	11:50:0/1:6,5:80,0,90	8:45:0/0:8,0:0,45,100	0:.:./.:0,0:.
+chr22	10591000	.	A	T	50	PASS	.	AD:PL:GT:DP:GQ	4,3:70,0,80:0/1:7:60	9,0:0,70,120:0/0:9:50	0,0:.:./.:0:.
+chr22	10592000	.	A	T	50	PASS	.	GT:DP:AB:GQ:AD:PL	0/1:12:0.42:70:7,5:90,0,100	0/0:10:0.01:60:10,0:0,60,120	./.:0:.:.:0,0:.
+chr22	10593000	.	A	T	50	PASS	.	GT:HQ:MIN_DP:SB	0/1:127,128:12:3,4,5,6	0/0:-129,20:8:8,0,0,0	./.:.,.:0:.,.,.,.
+chr22	10593500	.	A	T	50	PASS	.	GT:HQ:MIN_DP:SB	0/1:127,128:32767:3,4,5,6	0/0:-32760,32768:-32761:8,0,0,0	./.:32767,32768:0:127,128,32767,32768
+chr22	10594000	.	A	T	50	PASS	.	GT:AD:DP:GQ:PGT:PID:PL	0|1:4,5:9:50:0|1:P1:90,0,90	0/1:3,2:5:20:0|1:10594000_A_T_LONG_PHASE_SET:20,0,200	./.:0,0:0:.:.:.:.
+chr22	10595000	.	A	T	50	PASS	.	GT	0/1	1|1	./.
+chr22	10595500	.	A	T	50	PASS	.	GT	.|.	0|.	.|0
+chr22	10596000	.	A	T	50	PASS	.	GT	0	1	.
+chr22	10597000	.	A	C,G,T,AA,AC,AG,AT,CA,CC,CG	50	PASS	.	GT	10/10	0/10	./.

test/format-plan-empty-format-tag.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.3
+##contig=<ID=1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1
+1	1	.	A	C	.	PASS	.	GT::DP	0/1::5

test/format-plan-fallback.vcf

@@ -0,0 +1,10 @@
+##fileformat=VCFv4.3
+##contig=<ID=1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID">
+##FORMAT=<ID=QS,Number=1,Type=Float,Description="Quality score">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
+1	1	.	A	C	.	PASS	.	GT:PID:DP	0/1:AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA:12	0/0:P2:8	./.:.:0
+1	2	.	A	C	.	PASS	.	GT:DP	0/1	0/0:8	./.:0
+1	3	.	A	C	.	PASS	.	GT:QS:DP	0/1:1.5:999999999999999999999999999999	0/0:2.5:8	./.:.:0

test/format-plan-float-string.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.3
+##contig=<ID=1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype likelihoods">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2
+1	1	.	A	C,G	.	PASS	.	GT:GL:FT:DP	0/1:-0.25,-0.50,-0.75,-1.00,-1.25,-1.50:PASS:12	1/2:-0.50,-0.75,-1.00,-1.25,-1.50,-1.75:LowQual:8

test/format-plan-float-vector.vcf

@@ -0,0 +1,13 @@
+##fileformat=VCFv4.3
+##contig=<ID=1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype likelihoods">
+##FORMAT=<ID=QS,Number=.,Type=Float,Description="Variable-width quality scores">
+##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
+1	1	.	A	C	.	PASS	.	GT:GL:QS:AB:DP	0/1:-0.1,-1.2,-3:0.5,1.5:0.50:7	0/0:0,-5,-9:0.1,0.2,0.3,0.4:.:8	./.:.:1.25,2.5:.:0
+1	2	.	A	C,G	.	PASS	.	GT:GL:QS:AB:DP	1/2:-9,-8,-7,-6,-5,-4:0.1:0.25:12	0/2:-2,-3,-4,-5,-6,-7:0.2,0.3:0.75:9	./.:.:.:.:0
+1	3	.	G	T	.	PASS	.	QS:GT:GL:AB:DP	0.1,0.2:0/1:-1,-2,-3:0.5:5	.:0/0:0,-10,-20:0.0:4	0.3,0.4,0.5:./.:.:.:0
+1	4	.	T	G	.	PASS	.	GT:GL:QS:AB:DP	0/1:.:.:.:6	0/0:.:.:.:4	./.:.:.:.:0
+1	5	.	C	T	.	PASS	.	GT:GL:QS:AB:DP	0/1:-0.4,-0.8:0.1:0.5:3	0/0:0,-2:0.2:0.1:2	./.:.:.:.:0

test/format-plan-gt-header-shape.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.3
+##contig=<ID=chr22,length=50818468>
+##FORMAT=<ID=GT,Number=2,Type=String,Description="Malformed genotype header">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3
+chr22	10620000	.	A	T	50	PASS	.	GT:DP	0/1:7	0/0:5	./.:0