Also report position of 2nd read in "group --group-out" table#180

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fgp wants to merge 15 commits into

CGATOxford:masterfrom

Cibiv:group_endpos

Commits on Feb 29, 2020

Don't increment "Input Reads" twice for unmapped reads if return_unmapped is set.
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Removed redundant check for read.is_mapped
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Added get_readpairs, which returns properly paired reads as pairs (read1, read2)
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Added (trivial) get_singletons, which replaces get_readpairs if --paired is not specified
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Made get_bundles use get_readpairs to process mate pairs together
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In --paired mode, the "group" tool now reports the position of the 2nd mate
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Upated "dedup" to use the pair support in get_bundles instead of TwoPassPairWriter
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In --paired mode, apply the mapping quality filter to 2nd reads as well
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In --paired mode, use the mapping position, length and splicing of both reads as a grouping key
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Added test case count_paired_wide_contig with tests "count" in --paired mode
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Added test case dedup_paired_contig which tests "dedup" in --paired mode
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Added test case group_paired_contig which tests "group" in --paired mode
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Fixed get_readpairs to reports pairs in ascending mapping position of read1
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Added python3 versions of the tests dedup_paired_contig and group_paired_contig
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Use mapping position of read1 in addition to query name as a mate pair's key in get_readpairs
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