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Support for simultaneous reading of unindexed VCF/BCF files. #1089

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Merged
merged 3 commits into from
Jul 8, 2020
Merged

Support for simultaneous reading of unindexed VCF/BCF files. #1089

merged 3 commits into from
Jul 8, 2020
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pd3
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@pd3 pd3 commented Jun 24, 2020

In order for this to work, the caller must ensure that the input
files have chromosomes in the same order and consistent with the
order of sequences in the header.

Replaces #1076.

pd3 added a commit to samtools/bcftools that referenced this pull request Jun 24, 2020
@pd3
New merge --no-index option which allows to merge unindexed files.
eea66d7 
In order for this to work, the input files have chromosomes in the
same order and consistent with the order of sequences in the header.

Depends on samtools/htslib#1089.
This was referenced Jun 24, 2020
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@daviesrob
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Well, so far I've failed to fool the out-of-order detection logic, so I think this should be safe enough. I did notice that it isn't worried about POS not in order within a chromosome. It seems to work, albeit outputting out of order records, so presumably it's no more of a problem than for the single-file case?

Would you have any objection to me renaming BCF_SR_REQUIRE_IDX_WARN to something like BCF_SR_NO_INDEX_WARN? The current symbol seems a little wrong as it's describing the opposite of what's being asked for. I can handle the necesary changes if you're happy with that.

pd3 and others added 3 commits July 7, 2020 14:59
@pd3 @daviesrob
Support for simultaneous reading of unindexed VCF/BCF files.
6e0ed10 
In order for this to work, the caller must ensure that the input
files have chromosomes in the same order and consistent with the
order of sequences in the header.

Replaces #1076.
@daviesrob
Add synced reader no-index tests
818b271
@valeriuo
Fix paths for Windows tests.
832e4ba
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Rebased with added tests. BCF_SR_REQUIRE_IDX_WARN has been changed to BCF_SR_ALLOW_NO_IDX to better reflect what the option does. I'll adjust the bcftools part to match when this has gone in.

@daviesrob daviesrob merged commit 832e4ba into develop Jul 8, 2020
@daviesrob daviesrob deleted the bcf-no-idx branch July 8, 2020 09:27
daviesrob pushed a commit to samtools/bcftools that referenced this pull request Jul 8, 2020
@pd3
New merge --no-index option which allows to merge unindexed files. …

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365d117 
…(PR #1253)

In order for this to work, the input files have chromosomes in the
same order and consistent with the order of sequences in the header.

Depends on samtools/htslib#1089.
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