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latest_test_results
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CUnit - A Unit testing framework for C - Version 2.1-0
http://cunit.sourceforge.net/
Suite: Suite_1
Test: Check that bitfield as defined really is 64bits on this platform ... passed
Test: Test the assignment operator for BinaryKmers ... passed
Test: Test the comparison operator for binary kmers ... passed
Test: Test the less than operator for binary kmers ... passed
Test: Test the right shift operator for big binary kmers that are encoded in multiple long integers ... passed
Test: Test the left shift operator for big binary kmers that are encoded in multiple long integers ... passed
Test: test reading of fasta file ... passed
Test: test reading of long fasta file ... passed
Test: test reading of fastq file ... passed
Test: test reading of fastq file when some reads are too long or have bad characters ... Lengths of quality [22] and sequence [7] strings don't coincide for this read: [read2]. Skip it
passed
Test: test conversion from binary nucleotide to C string ... passed
Test: test binary kmer reverse complement ... passed
Test: test seq reverse complement ... passed
Test: test nucleotide iterator ... passed
Test: test creation of binary kmers from sequence - sliding window ... passed
Test: test shift last kmer to start ... passed
--Run Summary: Type Total Ran Passed Failed
suites 1 1 n/a 0
tests 16 16 16 0
asserts 292 292 292 0
CUnit - A Unit testing framework for C - Version 2.1-0
http://cunit.sourceforge.net/
Suite: Suite_1
Test: test hash_table_find_or_insert using Element from graph/ ... passed
Test: test hash_table_apply_or_insert using Element from graph/. This test takes a little while - do not panic if it takes a minute or two ... passed
--Run Summary: Type Total Ran Passed Failed
suites 1 1 n/a 0
tests 2 2 2 0
asserts 562219 562219 562219 0
CUnit - A Unit testing framework for C - Version 2.1-0
http://cunit.sourceforge.net/
Suite: Test main functionality of Cortex
Test: Test element - get edge copy ... passed
Test: Test assignment operator for element ... passed
Test: Test setting and checking of element status ... passed
Test: Test element - get coverage of node for specific person ... passed
Test: Test element -increment coverage for different people ... passed
Test: Test function checking number of edges to nodes with specified status ... passed
Test: Sanity test for hash_table_find - adding kmers to graph and finding them ... passed
Test: Test dumping and reloading of multicolour binary ... 5 kmers dumped to file ../data/tempfiles_can_be_deleted/dump_cortex_var_graph.ctx
43 kmers dumped to file ../data/tempfiles_can_be_deleted/dump_cortex_var_graph_3.ctx
passed
Test: Test dump Binary format version5, and reload ... 5 kmers dumped to file ../data/tempfiles_can_be_deleted/dump_cortex_var_graph.ctx.binversion5
43 kmers dumped to file ../data/tempfiles_can_be_deleted/dump_cortex_var_graph_3.ctx.binversion5
passed
Test: Test loading of a singlecolour binary ... passed
Test: Test loading of a single-colour binary where nodes are only loaded if they already exist in a predefined "clean" colour, and if so, only taking the edges that overlap both colours ... 11 kmers dumped to file ../data/tempfiles_can_be_deleted/dump_cortex_var_graph.clean.ctx
passed
Test: Test that coverage of kmers are correcty counted as reads are loaded from a file ... passed
Test: Test getting sliding windows, breaking when kmer is not in graph - internal function ... passed
Test: Test getting sliding windows breaking when kner or edge is not in graph - internal function ... passed
Test: Test function for getting length distribution of filtered/effective reads after N's, low quality, PCR duplicates and homopolymers have been cut or filtered ... passed
Test: Test checking if a path lies in a (function of) colours ... passed
Test: Test dumping of cleaned fasta by aligning against a cleaned graph ... passed
Test: Test removal of PCR duplicate reads from paired-end fastq ... passed
Test: Test removal of PCR duplicate reads from single-ended fastq ... passed
Test: Test loading of three binaries as dumped by graph into sv_trio as separate people ... passed
Test: Test utility function for getting supernode containing a given node ... passed
Test: Test that can identify supernode ends ... passed
Test: Test that can get the min and max coverage of a supernode ... passed
Test: Test function for checking if condition is true for all nodes in supernode ... passed
Test: Test error correction via topology of graph - tip clipping ... passed
Test: Test removal of low-coverage nodes ... passed
Test: Test utility function for applying some other function to all nodes in a path defined by a fasta ... passed
Test: Test get_perfect_path (maximal path without branches) in single colour of graph ... passed
Test: Loading two people, one fasta each, in same population, and print supernodes.
Each person has 2 reads, and we have manually determined what the supernodes should be ... passed
Test: Load three people in one population, each consists of one toy chromosome.
Find their individual supernodes correctly ... passed
Test: Load two people sharing an Alu, differing by sequene before and after the Alu. Find supernodes. ... passed
Test: Load two people in one population, and test that given a kmer, we can find the first node in the supernode in which that kmer lies. ... passed
Test: Load two people in one population, and test that given a node in a person's graoh, you can find the next node in the supernode. ...
please reimplement (not urgent as no current users of this code) conssensus code using db_graph_supernode NULL TEST
. passed
Test: Load two people in one population, and test that can pull out required subsection of a supernode. ...
please reimplement (not urgent as no current users of this code) conssensus code using db_graph_supernode NULL TEST
. passed
Test: Load two people in one population, and test that for each separately, can find the best sub_supernode, requiring certain people_coverage ... passed
Test: Check that correctly get stats on how many kmers are shared by 1,2,3,... people in a population ... passed
Test: Unit test of utilty function to produce array of nodes corresponding to a given path through graph, as specified by a fasta file ... passed
Test: Unit test of wrapper function for above utility function ... passed
Test: Test utility function to get next read from file and return it as an array of nodes ... passed
Test: Simple null test of new algorithm to find variants using trusted paths AND supernodes. Take a person whose genome is a single read, and a reference genome which is identical.
Algorithm should find no variants! ... passed
Test: Simple null test of new algorithm to find variants using trusted paths AND supernodes. Take a person whose genome is a single Alu, and a reference genome which is identical.
Algorithm should find no variants. ... passed
Test: Another null test of the Path Divergence/supernode SV caller. Reference and individual are identical again.
In this case they are both equal to an Alu, some N's, and then the same Alu again. Algorithm should find no variants.
Note this is testing something new - since the reference is essentially a repeat of an Alu, there is the risk that our algorithm would map the 3prime anchor onto the wrong copy of the repeat,
and falsely call an insertion between the start of the first copy, and the end of the second. ... passed
Test: Another null test of the Path Divergence/supernode SV caller. Reference and individual are identical - this time they are both equal to around 10kb taken from the start of Human chromosome 1.
Algorithm should find nothing. ... passed
Test: A targeted null test of the Path Divergence/supernode SV caller. The reference is a tandem repeat of about 36 bases; the individual has an Alu inserted between the two copies of the repeat.
Since the supernode in the individual has one copy of the repeat, then the Alu, and then stops, the algorithm should fail to attach a 3prime anchor, and fail to call the insertion. ... passed
Test: First simple (positive) test of the Path Divergence SV caller. Reference and individual are identical except for a single SNP.
Test that caller finds the SNP, correctly gives the coordinates in the reference, and gives the sequence of the 5prime, and 3prime anchors, and the two alternative branches (reference and individual). ... passed
Test: Test of the Path Divergence SV caller. Reference has two copies of the same Alu (genome is just those two Alu's plus some N's - nothing else) and the individual differs by a single base in one copy of the Alu.
Algorithm should call the SNP despite being in the Alu.
(Further, this is an example where we walk the supernode in the opposite direction to that in which it lies in our array - this therefore covers the other main code path in our implementation.) ... passed
Test: Test of the Path Divergence SV caller. Reference is a short sequence, and individual has a 2-base deletion.
Caller should spot this and correctly identify the coordinates in the reference, the flanking regions, and the sequence for the two branches ... passed
Test: Test of the Path Divergence SV caller. Reverse the roles of reference and individual in the previous test. Caller should spot the 2 base insertion
Identify the coordinates of variant start, and the relevant flank and branch sequences ... passed
Test: Test of the Path Divergence SV caller. Reference is a single supernode, and individual has a complete Alu inserted within the supernode. Find the insertion.
... passed
Test: Test of the Path Divergence SV caller. Reverse roles of reference/individual in previous test, and call deletion of Alu. ... passed
Test: Test of the Path Divergence SV caller. Reference has an Alu inserted within another Alu. Individual lacks the insertion.
Call the Alu insertion and correctly identify the coordinates of the variant, flanking sequences, and sequences of the two branches ... passed
Test: Test of the Path Divergence SV caller. Reference is about 10kb ofHuman chromosome 1, with about 1 kb of Human chromosome 2 inserted in the middle. Individual lacks the 1kb insertion.
Call the deletion, and correctly find maximal flanking regions, and identfy the sequence of the two branches ... passed
Test: Test of the Path Divergence SV caller. Identical to above test, but with 30kb of Human chromosome 12 added before sequence of above test
This test is purely to check that the code which loads chunks of data from the Path Divergence fasta bit by bit, works properly, and allows accurate determining of the correct variant location in the trusted fasta file. ... passed
Test: Test utility function for finding coverages of nodes that lie on one allele but not the other, in a variant. ... passed
Test: Test utility function for calculating read-arrivals on an allele ... passed
Test: Test calculation of genotype likelihoods for sites called by Bubble Caller ... passed
Test: Test reading of variant call output (full flank file) ... passed
Test: Test reading of variant call output (full flank file), when one branch < k long ... passed
Test: Test reading of variant call output (full flank file), when both branches < k long ... passed
Test: Test reading of variant call output (full flank file), when both branches < k long and zero-length 3p flank ... passed
Test: Test utility function for mutating specific bases in a string ... passed
Test: Test utility function for error-correcting reads to match a trusted graph ... passed
Test: Test utility function for checking kmers and qualities in a read that might need correction ... passed
Test: Test error correction of fastq files against a graph ... passed
Test: Test error correction utility function for greedy random walk ... passed
Test: Test error correction can output corrected reads in positive strand direction if desired ... passed
--Run Summary: Type Total Ran Passed Failed
suites 1 1 n/a 0
tests 66 66 66 0
asserts 12714 12714 12714 0