updatehtslib compare against masterpull #13
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…left out to make test pass for now
nalinigans
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nalinigans
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Looks great @eneskuluk. Please see comments.
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| /* Returns the appropriate handler, or NULL if the string isn't an URL. */ | ||
| static const struct hFILE_scheme_handler *find_scheme_handler(const char *s) | ||
| const struct hFILE_scheme_handler *find_scheme_handler(const char *s) |
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Can you see if there is a new api to use the htslib plugin mechanism for schemes like azb://.s3://, so we don't have to expose this function?
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There are new functions to list plugins and schemes. Explained here : samtools#1170 and samtools#1222. Not reviewed in depth yet.
htslib/vcf.h
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| #define BCF_HT_REAL 2 | ||
| #define BCF_HT_STR 3 | ||
| #define BCF_HT_LONG (BCF_HT_INT | 0x100) // BCF_HT_INT, but for int64_t values; VCF only! | ||
| #define BCF_HT_REAL 7 |
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Can you investigate if we add to the original definition instead of replacing them?
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Yeah, I think we can do that, keep the originals, replace what we use now in the new ones.
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I reverted changes to HT_REAL and HT_STR but HT_LONG requires more changes on our genomicsdb side(variant_operations.cc) as it is done according to being HT_LONG not that high value. I might need to take a look a bit more.
htslib/vcf.h
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| #define VCF_OVERLAP (1<<5) // overlapping deletion, ALT=* | ||
| #define VCF_INS (1<<6) // implies VCF_INDEL | ||
| #define VCF_DEL (1<<7) // implies VCF_INDEL | ||
| #define VCF_OTHER 32 |
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Not sure why we need to be different from the origin vcf.h here. @mlathara any ideas?
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Seems to work just fine with default values. Passes all tests when it is like following, all values are default except the ones we added:
#define VCF_REF 0
#define VCF_SNP (1<<0)
#define VCF_MNP (1<<1)
#define VCF_INDEL (1<<2)
#define VCF_OTHER (1<<3)
#define VCF_BND (1<<4) // breakend
#define VCF_OVERLAP (1<<5) // overlapping deletion, ALT=*
#define VCF_INS (1<<6) // implies VCF_INDEL
#define VCF_DEL (1<<7) // implies VCF_INDEL
#define VCF_ANY (VCF_SNP|VCF_MNP|VCF_INDEL|VCF_OTHER|VCF_BND|VCF_OVERLAP|VCF_INS|VCF_DEL) // any variant type (but not VCF_REF)
#define VCF_NON_REF (1<<8)
#define VCF_SPANNING_DELETION (1<<5)
kstring.c
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| if (*ep == '.') { | ||
| if (z[-1] == '.') | ||
| z[-1] = 0; | ||
| if (z[-1] == '.'){ |
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this will be reverted back to original, this is where it was keeping fraction part for .0 values.
vcf.c
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| v->rlen = val1 - v->pos; | ||
| } | ||
| } else if ((y>>4&0xf) == BCF_HT_REAL) { | ||
| } else if ((y >> 4 & 0xf) == BCF_HT_REAL) { |
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Same as original! No need for the change.
vcf.c
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| // Ensure string we parse has space to permit some over-flow when during | ||
| // parsing. Eg to do memcmp(key, "END", 4) in vcf_parse_info over | ||
| // the more straight forward looking strcmp, giving a speed advantage. | ||
| /* |
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Remove extra line as we will try to make the patch as minimal as possible.
vcf.c
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| s->s[s->l+2] = 0; | ||
| s->s[s->l+3] = 0; | ||
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| for(int i = 0; i < 4; i++) |
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Functionally same as original, we should probably remove this.
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Those were running in the original but the we way we use it in the parse_info functions breaks it. I'll make sure to remove those.
htslib/vcf.h
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| else{ | ||
| *p++ = 1<<4|BCF_BT_INT64;// | ||
| i64_to_le(size,p); | ||
| s->l += 10; // not so sure about +10 here, whether it is accurate or changes anything. |
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Do you think this line of code accurate @nalinigans ? Not sure how x in s->l += x determined.
faidx.c
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| } | ||
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| s[l] = '\0'; | ||
| *len = l < INT_MAX ? l : INT_MAX; |
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this line needs to change as well, remnant from old code.
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