8000 `vcf_parse()` fails · Issue #358 · samtools/htslib · GitHub
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noporpoise opened this issue Mar 20, 2016 · 3 comments
Closed

vcf_parse() fails #358

noporpoise opened this issue Mar 20, 2016 · 3 comments

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@noporpoise
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vcf_parse fails with the following error:

[E::vcf_parse_format] Invalid character '?' in 'GT' FORMAT field at 1:25

Here is a short example:

char hdrstr[] = "##fileformat=VCFv4.2\n"
"##FILTER=<ID=PASS,Description=\"All filters passed\">\n"
"##fileDate=20160317\n"
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"
"##reference=ref.fa\n"
"##contig=<ID=1,length=50,assembly=ref>\n"
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tMrT\n";

char vline[] = "1\t25\t.\tC\tT\t.\tPASS\t.\tGT\t0/1\n";

Code to parse strings hdrstr and vline into bcf_hdr_t and bcf1_t objects then print them out:

#include "htslib/vcf.h"

#define die(fmt,...) do { \
  fprintf(stderr, "[%s:%i] Error: %s() "fmt"\n", __FILE__, __LINE__, __func__, ##__VA_ARGS__); \
  exit(EXIT_FAILURE); \
} while(0)

...

fprintf(stdout, "%s%s\n", hdrstr, vline);
bcf1_t *v = bcf_init();
bcf_hdr_t *hdr = bcf_hdr_init("w");
if(bcf_hdr_parse(hdr, hdrstr) != 0) die("Cannot construct VCF header");
size_t vlen = strlen(vline);
kstring_t ks = {.l = vlen, .m = vlen, .s = vline};
if(vcf_parse(&ks, hdr, v) != 0) die("Cannot construct VCF entry: '%s'", vline);
memset(&ks, 0, sizeof(ks));
if(vcf_format(hdr, v, &ks) != 0) die("vcf_format failed");
int hdrslen = 0;
char *outhdr = bcf_hdr_fmt_text(hdr, 0, &hdrslen);
fprintf(stdout, "%s%s", outhdr, ks.s);
free(outhdr);
free(ks.s);
bcf_destroy(v);
bcf_hdr_destroy(hdr);

Compile:

gcc -Wall -Wextra -I../htslib -o vtest vtest.c ../htslib/libhts.a -lz

The vcf_parse() line fails with the above error.

Apologies: this issue was originally posted to bcftools issue tracker by mistake.
@noporpoise noporpoise mentioned this issue Mar 20, 2016
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@noporpoise
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ed35e41 appears to be the offending commit. The above test passes on previous commits and fails on this one. Am I doing something wrong or is vcf_parse() really broken?

@jmarshall
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This is failing because vcf_parse() does not expect to see \n in its input string.

@noporpoise
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That fixed it - thank you @jmarshall. I've suggested a pull request to update to the function documentation.

jmarshall added a commit that referenced this issue Mar 29, 2016
@jmarshall
Add BCF_ERR_CHAR bcf1_t::errcode and improve diagnostic
3857875 
Show the exact invalid character for unprintable characters too;
improves error messages such as in #358.
charles-plessy added a commit to Debian/htslib that referenced this issue Apr 25, 2016
@charles-plessy
Merge tag '1.3.1' into debian/unstable
36bf59a 
HTSlib release 1.3.1: bug fix release, notably error checking

* Improved error checking and reporting, especially of I/O errors when
  writing output files (samtools#17, samtools#315, PR samtools#271, PR samtools#317).

* Build fixes for 32-bit systems; be sure to run configure to enable
  large file support and access to 2GiB+ files.

* Numerous VCF parsing fixes (samtools#321, samtools#322, samtools#323, samtools#324, samtools#325; PR samtools#370).
  Particular thanks to Kostya Kortchinsky of the Google Security Team
  for testing and numerous input parsing bug reports.

* HTSlib now prints an informational message when initially creating a
  CRAM reference cache in the default location under your $HOME directory.
  (No message is printed if you are using $REF_CACHE to specify a location.)

* Avoided rare race condition when caching downloaded CRAM reference sequence
  files, by using distinctive names for temporary files (in addition to O_EXCL,
  which has always been used).  Occasional corruption would previously occur
  when multiple tools were simultaneously caching the same reference sequences
  on an NFS filesystem that did not support O_EXCL (PR samtools#320).

* Prevented race condition in file access plugin loading (PR samtools#341).

* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
  Continue anyway" warning messages (samtools#299).

* Various minor CRAM fixes.

* Fixed documentation problems samtools#348 and samtools#358.
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