phasemerge: *_collapsed.txt and *_summary.txt report different number of loci #16
Description
When running phasemerge the resulting summary folder contains _collapsed.txt and _summary.txt both listing predicted phas loci. However they differ in the number of reported loci regardless of the used parameter and and libraries, with the summary.txt loci being a subset of collapsed.txt.
For example:
21PHAS_p1e-06_collapsed.txt:
Name p-val Chr Start End Strand Lib
Phas-1 1e-07 1 18549462 18549648 NONE nd
Phas-2 1e-07 1 23178442 23178628 NONE nd
Phas-3 1e-07 1 23299603 23299831 NONE nd
Phas-4 1e-07 1 23413412 23413682 NONE nd
Phas-5 1e-07 1 23419942 23420149 NONE nd
Phas-6 1e-07 1 23490185 23490371 NONE nd
Phas-7 1e-07 1 23507890 23508076 NONE nd
Phas-8 5e-07 2 11721883 11722090 NONE nd
Phas-9 1e-07 2 16539751 16540000 NONE nd
Phas-10 5e-07 5 23394349 23394430 NONE nd
21PHAS_p1e-06_summary.txt
Name P-val Chr Start End Identifier Best k-val Phasi ratio Max Tag Ratio SRR1634280.fa Total Phasi Abundance Most Abun Tag (MAT) MAT Abun MAT2 MAT2 Abun BestLib
Phas-1 1e-07 1 18549462 18549649 1_18549462_18549648 15 0.92 0.25 1484 1484 TATTATCAGAGTAGTTATGAT 368 TTCTAAGTCCAACATAGCGTA 340 nd
Phas-3 1e-07 1 23299603 23299832 1_23299603_23299831 11 0.84 0.46 699 699 ATGGGATATAAACCTGATACC 323 AACGGATTATGTAAGAGAGGT 115 nd
Phas-5 1e-07 1 23419942 23420150 1_23419942_23420149 10 0.84 0.46 700 700 ATGGGATATAAACCTGATACC 323 AACGGATTATGTAAGAGAGGT 115 nd
Phas-8 5e-07 2 11721883 11722091 2_11721883_11722090 14 0.87 0.33 1129 1129 ATGATATTTGTAGTAATGGCG 373 TTCTAAGTCCAACATAGCGTA 340 nd
Phas-9 1e-07 2 16539751 16540001 2_16539751_16540000 21 0.91 0.45 5252 5252 TTTGAACTTGTGTATTTTGAA 2338 TCCAAGCGAATGATGATACTT 1347 nd
Is there a reason for this?
Note, I've specified a pvalue of 0.01 (and tried few more setttings), so this is not the discriminating factor as can also be seen above.
It would be nice if _summary.txt would contain the complete _collapsed.txt list since it contains useful additional information for each loci.