samtools 64 bit support #1117
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samtools 64 bit support #1117
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valeriuo
reviewed
Oct 7, 2019
valeriuo
reviewed
Oct 7, 2019
valeriuo
reviewed
Oct 23, 2019
bam_markdup.c
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| int32_t orientation, leftmost; | ||
| hts_pos_t this_coord, this_end, other_coord, other_end; | ||
| int32_t this_ref, other_ref; | ||
| int8_t orientation, leftmost; |
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leftmost could end up with the wrong sign, due to truncation.
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That's true. The uses of leftmost should be separated out in that function.
Separate tid from pos in heap1_t. Merge rev with pos as only one bit is needed. Radix sort is changed to work exclusively on bytes instead of SHIFT bits at a time. It now counts the number of bytes needed to store pos and tid separately, which should make it more efficient when pos is small.
Use bedidx.h in bam2depth.c and bam_plcmd.c for bed_* function prototypes.
Tests for round-trip, index, bedidx, sort, merge, depth, and tview. Unrelated fix of "my variable $f masks earlier declaration" warning.
This checks various boundary locations rather than just +10Gb to all and also validates fixmates generation of PNEXT and TLEN as well as samtools sort.
Added another smaller variable for the stored value.
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Make samtools work with 64 bit positions, now HTSlib supports them.
Looked at so far are
sort,merge,depth,tviewand the BED file reader. This is a work-in-progress, more sub-commands will be added.Includes tests as it's easy to otherwise miss places where 32-bitness has crept in.
Later additions:
stats,markdup,calmd,fixmate,faidx,mpileup,depad,targetcut,coverage