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ocxtal / minialign

[IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long reads
MIT License
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No SAM header #10

Closed colindaven closed 7 years ago

colindaven commented 7 years ago

Hi,

I could run my ONT data through the tool fine.

However the SAM output completely lacks a SAM header. This will make it difficult to do BAM conversion, call SNPs, view in genome browser etc. Is this planned ?

minimap -V 0.2-r123

ocxtal commented 7 years ago

Actually the current minialign outputs the general sam header as follows:

ref: E. coli MG1655

@HD     VN:1.0  SO:unsorted
@SQ     SN:gi|556503834|ref|NC_000913.3|        LN:4641652
@PG     ID:minialign    PN:minialign
S1_623  0       gi|556503834|ref|NC_000913.3|   4439847 60      6S29M1I6M1I11M1I12M1I33M1D7M1I13M...

ref: human hg38

@HD     VN:1.0  SO:unsorted
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr10        LN:133797422
@SQ     SN:chr11        LN:135086622
...
@SQ     SN:chrX LN:156040895
@SQ     SN:chrY LN:57227415
@SQ     SN:chrY_KI270740v1_random       LN:37240
@PG     ID:minialign    PN:minialign
f3920def-68ae-4956-8900-6398064c4f93_Basecall_Alignment_template        4       *       0       0...

Please check the version number hitting minialign -v and if it says like 0.5.3 or 0.5.2-16-gb6abbc2, it should supports the three types of the headers, @HD, @SQ, and @PG. If you need another specific header line please inform me of it.

Thanks,

colindaven commented 7 years ago

Sorry, my mistake ! Too many minis around.

Analyzed the same sample with minimap/miniasm previously and got mixed up.

Thanks