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jkbonfieldwhitwham
jkbonfield
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whitwham
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Add tests for CRAM TLEN generation.
We convert from previously built CRAM files that don't use the detached flag to SAM files, validating all the auto-TLEN generation code. Note however some of this code is arbitrary, so the SAM files are not the only valid decoded versions of these CRAM files. The tests here are primarily for regression testing purposes, so we don't accidentally change behaviour without realising. If we subsequently improve our methods of resolving ties (especially around triplets) then we would edit the SAM files too. Note to build the CRAM files from the SAM files I disabled the "detached" enabling part of the CRAM encoder with this patch: diff --git a/cram/cram_encode.c b/cram/cram_encode.c index 6fe797a..2ede0359 100644 --- a/cram/cram_encode.c +++ b/cram/cram_encode.c @@ -3881,6 +3881,7 @@ static int process_one_read(cram_fd *fd, cram_container *c, } } + detached: /* * The fields below are unused when encoding this read as it is * no longer detached. In theory they may get referred to when @@ -3940,7 +3941,7 @@ static int process_one_read(cram_fd *fd, cram_container *c, kh_val(s->pair[sec], k) = rnum; } else { - detached: + detached_: //fprintf(stderr, "unpaired\n"); /* Derive mate flags from this flag */
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‎Makefile‎

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@@ -699,6 +699,7 @@ check test: all $(HTSCODECS_TEST_TARGETS)
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cd test/mpileup && ./test-pileup.sh mpileup.tst
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cd test/fastq && ./test-fastq.sh
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cd test/base_mods && ./base-mods.sh base-mods.tst
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cd test/tlen && ./tlen.sh tlen.tst
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REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
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test/test-regidx
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cd test && \

‎test/tlen/README‎

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ref AAAAACCCCCGGGGGTTTTT
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12345678901234567890
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Test files for read pairs.
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Starting letter:
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a = both start/end differ
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b = only ends differ
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c = only start differ
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d = both start/end match
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Each file has two versions (eg a7 and a7b) which are identical except
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for read ordering with the entries swapping lines. (This may make some
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data unsorted.)
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We also have neighbouring pairs (a7/a8, a9/a10) which are the same
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coordinates, but flipping the orientation of READ1 and READ2.
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Eg pointing inwards vs pointing outwards.
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Starts and ends differ:
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Combinations: (2) R1 before R2?
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(2) R1 starts before R2?
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(2) R1 ends before R2?
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(2) R1 top, R2 bottom (vs vice versa)?
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=> 16
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a7 a8
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1---> <---1
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<---2 2--->
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2---> <---2
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<---1 1--->
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a7b a8b
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<---2 2--->
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1---> <---1
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<---1 1--->
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2---> <---2
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a9 a10
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1------> <------1
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<--2 2-->
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2------> <------2
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<--1 1-->
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a9b a10b
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<--2 2-->
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1------> <------1
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<--1 1-->
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2------> <------2
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Starts match, ends differ:
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b7 b8
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1---> <---1
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<------2 2------>
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2---> <---2
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<------1 1------>
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b7b b8b
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<------2 2------>
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1---> <---1
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<------1 1------>
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2---> <---2
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Starts differ, ends match:
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c7 c8
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1------> <------1
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<---2 2--->
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2------> <------2
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<---1 1--->
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c7b c8b
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<---2 2--->
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1------> <------1
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<---1 1--->
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2------> <------2
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Starts and ends both match:
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d7
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1------>
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<------2
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2------>
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<------1
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d7b
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<------2
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1------>
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<------1
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2------>
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-----------------------------------------------------------------------------
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Test files for read triplets
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d4 d5
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1-----> <-----1
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<-----m <-----m
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<-----2 2----->
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d4b d5b
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1-----> <-----1
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<-----2 2----->
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<-----m <-----m
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d4c d5c
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<-----2 2----->
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<-----m <-----m
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1-----> <-----1
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d4d d5d
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<-----2 2----->
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1-----> <-----1
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<-----m <-----m
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d4e d5e
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<-----m <-----m
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1-----> <-----1
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<-----2 2----->
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d4f d5f
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<-----m <-----m
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<-----2 2----->
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1-----> <-----1
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a4 a5
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1---> m--->
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m---> 1--->
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<---2 <---2
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‎test/tlen/a4.cram‎

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‎test/tlen/a4.sam‎

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@SQ SN:ref LN:20
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seq 65 ref 3 0 7M = 6 13 AAACCCC IIIIIII
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seq 225 ref 6 0 7M = 9 -13 CCCCCGG IIIIIII
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seq 145 ref 9 0 7M = 3 -13 CCGGGGG IIIIIII

‎test/tlen/a5.cram‎

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‎test/tlen/a5.sam‎

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@SQ SN:ref LN:20
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seq 193 ref 3 0 7M = 6 13 AAACCCC IIIIIII
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seq 97 ref 6 0 7M = 9 -13 CCCCCGG IIIIIII
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seq 145 ref 9 0 7M = 3 -13 CCGGGGG IIIIIII

‎test/tlen/a7.cram‎

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‎test/tlen/a7.sam‎

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@SQ SN:ref LN:20
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seq 97 ref 3 0 11M = 6 14 AACCCCCGGGG IIIIIIIIIII
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seq 145 ref 6 0 11M = 3 -14 CCCCGGGGGTT IIIIIIIIIII
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seqr 161 ref 3 0 11M = 6 14 AACCCCCGGGG IIIIIIIIIII
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seqr 81 ref 6 0 11M = 3 -14 CCCCGGGGGTT IIIIIIIIIII

‎test/tlen/a7b.cram‎

533 Bytes
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‎test/tlen/a7b.sam‎

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@SQ SN:ref LN:20
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seq 145 ref 6 0 11M = 3 -14 CCCCGGGGGTT IIIIIIIIIII
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seq 97 ref 3 0 11M = 6 14 AACCCCCGGGG IIIIIIIIIII
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seqr 81 ref 6 0 11M = 3 -14 CCCCGGGGGTT IIIIIIIIIII
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seqr 161 ref 3 0 11M = 6 14 AACCCCCGGGG IIIIIIIIIII

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